have you read this thread / articles yet? some interesting reading, it may be that FRAPS is not all that accurate anyway, even when it's telling you everything is fine...
http://forums.overclockers.co.uk/showthread.php?t=18500294
I have read the articles and they are indeed interesting reading. FRAPS is a handy tool but like you point out is isn't always accurate. Though it did bring to the fore the discussions about frame-times in multi-gpu. Finally AMD are going to attempt to address the stutter issues plaguing Crossfire out of the box.
As I have shown it can be fixed/reduced to much more acceptable levels but it would be nice if there was no need for messing with 3rd party tools.