This flip-flop works when facing north or south (lime wool) but not east or west (orange wool).
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Confirmed.

I've also been able to recreate the problem, but while the original post's problem is with East/West, mine is with North/South. (found in 1.7.2)
I made a short video on the issue: http://youtu.be/jBeF3aFxqpM
Hoping this will be fixed soon.

Still a bug in the latest Minecraft. Affected versions has been updated.

This is caused by the order in which the blocks are updated, and I believe it to be the same issue as MC-11165.