I'm sure there are many that have had headaches over this - you spent hours doing "find and replace" jobs throughout your project only to find that despite an errorless build you have the red squigglies all over the place...and I'm sure you have also found that the solution is to change the tag prefix in the web.config from asp to something like Ajax.
Well the bug is official! read more about it here on Scott Gu's blog.
Basically he suggests to do the above with the tag prefix or (as the bug only rears its head on content pages of a master page) have the master page open at all times.
Personally I think I'll be sticking with changing the tag prefix....I think it makes the markup easier to read and navigate anyway.