I am having the same issue. However, everything does work on startup and
continues to work until calling wpa_supplicant manually or ifdown.
Additionally, it can be 'fixed' by removing the driver module (I'm using
b43) and re-inserting it, then running /etc/init.d/networking restart.
While it is 'working', iwlist scanning returns nothing. I'm also
attaching the results from running wpa_supplicant -ddd. It seems to me
that it isn't necessarily an issue in WPA but in the driver (at least in
my case), as it is failing to get anything from an AP scan. Hope that
helps someone!

Cheers,
Christopher
Initializing interface 'wlan0' conf '/etc/wpa_supplicant.conf' driver 'wext' 
ctrl_interface 'N/A' bridge 'N/A'
Configuration file '/etc/wpa_supplicant.conf' -> '/etc/wpa_supplicant.conf'
Reading configuration file '/etc/wpa_supplicant.conf'
Line: 1 - start of a new network block
ssid - hexdump_ascii(len=8):
     53 4b 59 32 39 30 36 39                           SKY29069        
scan_ssid=1 (0x1)
key_mgmt: 0x2
PSK (ASCII passphrase) - hexdump_ascii(len=8): [REMOVED]
PSK (from passphrase) - hexdump(len=32): [REMOVED]
Priority group 0
   id=0 ssid='SKY29069'
SIOCGIWRANGE: WE(compiled)=22 WE(source)=21 enc_capa=0xf
  capabilities: key_mgmt 0xf enc 0xf flags 0x0
WEXT: Operstate: linkmode=1, operstate=5
Own MAC address: 00:0c:e5:53:12:da
wpa_driver_wext_set_wpa
wpa_driver_wext_set_key: alg=0 key_idx=0 set_tx=0 seq_len=0 key_len=0
wpa_driver_wext_set_key: alg=0 key_idx=1 set_tx=0 seq_len=0 key_len=0
wpa_driver_wext_set_key: alg=0 key_idx=2 set_tx=0 seq_len=0 key_len=0
wpa_driver_wext_set_key: alg=0 key_idx=3 set_tx=0 seq_len=0 key_len=0
wpa_driver_wext_set_countermeasures
wpa_driver_wext_set_drop_unencrypted
RSN: flushing PMKID list in the driver
Setting scan request: 0 sec 100000 usec
WPS: UUID based on MAC address - hexdump(len=16): 7a 5a 5b ef 7b 8b 56 a3 90 25 
20 26 76 fa 9f 26
WPS: Build Beacon and Probe Response IEs
WPS:  * Version
WPS:  * Wi-Fi Protected Setup State (0)
WPS:  * Version
WPS:  * Wi-Fi Protected Setup State (0)
WPS:  * Response Type (2)
WPS:  * UUID-E
WPS:  * Manufacturer
WPS:  * Model Name
WPS:  * Model Number
WPS:  * Serial Number
WPS:  * Primary Device Type
WPS:  * Device Name
WPS:  * Config Methods (0)
WPS:  * RF Bands (3)
EAPOL: SUPP_PAE entering state DISCONNECTED
EAPOL: KEY_RX entering state NO_KEY_RECEIVE
EAPOL: SUPP_BE entering state INITIALIZE
EAP: EAP entering state DISABLED
Added interface wlan0
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b06 len=12
State: DISCONNECTED -> SCANNING
Starting AP scan (specific SSID)
Scan SSID - hexdump_ascii(len=8):
     53 4b 59 32 39 30 36 39                           SKY29069        
Trying to get current scan results first without requesting a new scan to speed 
up initial association
Received 0 bytes of scan results (0 BSSes)
Cached scan results are empty - not posting
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 0 sec 0 usec
Starting AP scan (broadcast SSID)
Scan requested (ret=0) - scan timeout 5 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
EAPOL: disable timer tick
Starting AP scan (specific SSID)
Scan SSID - hexdump_ascii(len=8):
     53 4b 59 32 39 30 36 39                           SKY29069        
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
Starting AP scan (broadcast SSID)
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
Starting AP scan (specific SSID)
Scan SSID - hexdump_ascii(len=8):
     53 4b 59 32 39 30 36 39                           SKY29069        
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
Starting AP scan (broadcast SSID)
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
Starting AP scan (specific SSID)
Scan SSID - hexdump_ascii(len=8):
     53 4b 59 32 39 30 36 39                           SKY29069        
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
Starting AP scan (broadcast SSID)
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
Starting AP scan (specific SSID)
Scan SSID - hexdump_ascii(len=8):
     53 4b 59 32 39 30 36 39                           SKY29069        
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
Starting AP scan (broadcast SSID)
Scan requested (ret=0) - scan timeout 30 seconds
RTM_NEWLINK: operstate=0 ifi_flags=0x1003 ([UP])
RTM_NEWLINK, IFLA_IFNAME: Interface 'wlan0' added
Wireless event: cmd=0x8b19 len=16
Received 0 bytes of scan results (0 BSSes)
CTRL-EVENT-SCAN-RESULTS 
Selecting BSS from priority group 0
Try to find WPA-enabled AP
Try to find non-WPA AP
No suitable AP found.
Setting scan request: 5 sec 0 usec
CTRL-EVENT-TERMINATING - signal 2 received
Removing interface wlan0
State: SCANNING -> DISCONNECTED
wpa_driver_wext_set_operstate: operstate 0->0 (DORMANT)
WEXT: Operstate: linkmode=-1, operstate=5
No keys have been configured - skip key clearing
EAPOL: External notification - portEnabled=0
EAPOL: External notification - portValid=0
wpa_driver_wext_set_wpa
wpa_driver_wext_set_drop_unencrypted
wpa_driver_wext_set_countermeasures
No keys have been configured - skip key clearing
Cancelling scan request
Cancelling authentication timeout
WEXT: Operstate: linkmode=0, operstate=6

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