I confirmed the package"4.2.6.p3+dfsg-1ubuntu3.9" solved the problem in
Ubuntu Precise

NTP Version : 1:4.2.6.p3+dfsg-1ubuntu3.1

With no IPTABLES rule ==> Working
$ ntpdate x.x.x.x
11 Feb 16:15:19 ntpdate[1243]: adjust time server x.x.x.x offset 0.190571 sec

With IPTABLES rule ==> Not working
$ iptables -t nat -A POSTROUTING -p UDP --dport 123 -j SNAT --to-source 
y.y.y.y:100-122

$ntpdate x.x.x.x
11 Feb 16:15:36 ntpdate[1253]: no server suitable for synchronization found

With ntp (precise-proposed) + IPTABLE rules ==> Now working

NTP version: 1:4.2.6.p3+dfsg-1ubuntu3.9

$ iptables -t nat -A POSTROUTING -p UDP --dport 123 -j SNAT --to-source
y.y.y.y:100-122

$ ntpdate x.x.x.x
11 Feb 16:21:26 ntpdate[1986]: adjust time server x.x.x.x offset 0.005394 sec

Eric


** Tags added: verification-done-precise

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https://bugs.launchpad.net/bugs/1479652

Title:
  [patch] ntpd rejects source UDP ports less than 123 as bogus

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