What version are you using (I am at V3 beta)? Are you running in the loop or out in front (are switches set appropriately)?
IMHO, I had to revert to running the MF in front. I have a Mark V (serial loop) and some of the effects were just too much while running the MF in the loop. Granted, running a clean sound would make little difference, but when using the amp's distortion, I could never get the phaser and flangers to sound right to me. It was like it took over the sound of my amp for lack of a better description – like I lost the punch out of the preamp. Also, the chorus's (with the classic being an exception) sound horribly bright to me. Again, these are my opinions.
You might try the Rotary, that is becoming one of my favorite effects. Bank 6.1 (slow) if I remember correctly. It sounds good with the preamp at mild overdrive or heavy gain.
