I think the problem with scenarios is the group detection. I just tried r1221 with only the option for collection while solo disabled and it didn't collect any data. Once I enabled solo collection it worked fine.
do you read the tickets that are created on the WowAce project? Because today I noticed the one described here and it seems like it's an easy fix.
Or at least an easy workaround, because I'm wondering where the non-integer numbers come from. Seems weird.
You shouldn't leave CPU measurement addons running during fights. If one is measuring, everything results in by far more CPU usage. Do you have performance problems without running a measurement addon?
Also, you shouldn't trust these addons 100%. Recount needs to call an huge amout of functions during a fight (x functions for each combat log line) and these addons tend to show more CPU usage than there really is for many function calls.