I can't upvote on comments on SO or here on Meta. If I mouse over a comment I don't see any option to upvote or flag.
I can upvote and flag comments on SF and WebApps.
Using IE 8 (8.0.6001.18702).
For IE8 users who have this problem who also think that clearing your browser cache didn't help:
When you use the Delete Browsing History dialog in IE8, make sure you clear the checkbox for the 'Preserve Favorites website data' option before you click the Delete button!
Of course this won't help if SO isn't in your Favorites.