Can you take a screenshot of the problem?
Okay, that doesn't necessarily look like an egregious malfunction or anything, but I do see the difference. Honestly, I don't have a lot of experience with Acrobat page transitions, but it seems believable that once transitioning is active, the rendering engine might assume a different mode of operation (anti-aliasing) than it runs while displaying static pages of vector-based content.
A couple things you could try:
- Post this on the Acrobat forum, where it might be more likely to reach a seen-this-before audience
- Visit the Rendering section of Acrobat's Preferences dialog (Edit > Preferences > Page Display...), and try changing one setting at a time, then testing for a different result