I've had this before and it just went away, so I can't tell you what I did. BUT:
If I have a conditional statement using "is_single()" in my index.php, it doesn't work. Moving it to any other template page (like sidebar.php, for example) works fine.
Also, using something like "is_home()" or "is_category()" works fine.
Any guidance as to what I can look for. I'd have to assume it's something in the template, and probably something to do with the loop or a "$post change"...