Your flashed PCM is probably the cause of the herky-jerkies with cruise control. Basically what happens with a performance program is the Accelerator Pedal (and cruise control) signal is a lot more sensitive. There's only so much pedal range to use, and each little bit equals a larger bit of HP with a performance program, so you get more variation with the cruise. You didn't say how hot a program you have.
I recently put in one of Jody's 80 HP PCM's. I have a real touchy pedal especially in the lower gears, and notice that the cruise isn't as steady as it was with the stock PCM. It shows up most when going downgrade, essentially with the cruise calling for no power.
If you can't live with it, I'd suggest you get hold of Jody.