Ah!! Yes.  This is a known issue.

Earlier kernels ( <2.6.30) exported the interface but never actually
suspended the devices. The actual suspend really started from 2.6.30 and
above.

And what you are seeing might be only with a set of USB devices, not
all. Mostly it is the input keyboard/mouse driver (many of which are
broken).

This is fixed upstream but I think, for Ubuntu, you might have to wait
for the next release.

For details: See Debian BTS #535051


For now, just disable the USB suspend module in laptop-mode-tools

-- 
usb autosuspend disconnects usb devices at logon
https://bugs.launchpad.net/bugs/469517
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