Avoron |
A rogue with uncanny dodge can still lose her Dexterity bonus to AC if an opponent successfully uses a feint action against her. (Core Rulebook 69) Improved uncanny dodge makes no difference, except that the rogue cannot be flanked.
You do bring up an important point, which is that there is a definite difference between being flat-footed and losing your Dex bonus to AC. Unless something explicitly uses the words "flat-footed," assume that it doesn't make a character flat-footed.