AE CS4 Win works perfectly here under Boot Camp. Haven't tried it on Parallels.
I'm using AE on Win via Bootcamp on a MBR with good success.
But, as i'm doing a lot of timelapse, I know it's a pain to remove flicker, and I try as I can to prepare the shots so I will have close to no flickering.
But this phenomenon can't be avoided fom times to time.
So here is how i fix my flicking problems:
I use Maltaannon's CE Pixel Sampler which is a nice custom effet when you need to analyse the color. I add a adjustement layer and then I define a sample region where the picture is easily "readable " (a full color for exemple) and flicker visible.
And finally, with a little expression (I haven't the project at home with me so I don't have the specifics, but if you whatch maltaannon's tut on how the custom effect works, everything is in it) I link it to an exposure effect or a brightness/contrast (depends) to average it. Works great most of time
Works fine with Bootcamp on a Macbook Pro, but should not be a problem with Parallels, either. Especialyl the latest versions seem to offer resource management down to the microscopic level (number of threads/ cores, memory allocation, priority management), so I would guess if you tilt the balance to 90% usage for the virtual system, you won't see much of a difference compared to booting it natively.