There are many things that can cause that issue.
The most likely IMO is something going on in the background with Windows. I believe with my laptop it had something to do with Windows accessing the Paging File and caused my CPU to be pretty much useless.
Depends on the CPU you're talking about. IIRC you're running an older Athlon 64 X2 in which case all you have to do is go into your BIOS and turn off Cool n' Quiet. Same applies to the newer Phenoms and Athlon IIs, but those also have additional processor states that can be configured with for smoother computer operation. If you're on the Intel side of the house things are a bit different. Core 2's only have a low power state or whatnot, basically very similar to Cool n' Quiet but causes less issues for whatever reason. Go to CPUs like Nehalem or Sandy Bridge and then Intel has this whole mess of CPU states that are controlled by the load according to the scheduler or something like that (too tired to go look it up). Granted the only ones that really cause an issue are C0 and C1. Of course the more featured your Mobo is the better control you have over how that stuff actually works.
Now, why Reaper wouldn't have the issue and FL would is beyond me, but I can think of a couple of reasons as to why. Regardless though, it isn't really all that important if you just keep power saving stuff off in the first place though.