If your buttons are parented to the default bags (ContainerFrame1 etc), it's possible you're experiencing the toplevel/framestrata bug reported in this thread:
http://www.wowinterface.com/forums/s...ad.php?t=53715
Try ContainerFrame1:SetToplevel(false) and see if they start obeying again.
That said, in my experiments I did not see any issues with frame level. It was just strata misbehaving.