I am using Melodyne for pitch correction on a vocal track which consists of many separately recorded clips. My method is to take small sections and do the pitch correction, then audition the results and move onto the next section. What I've discovered is that this results in some of the audio shifting about a half second earlier after having been corrected. If I disable Melodyne from the effects bin the problem goes away. It is clearly related to the effect. 
 
Is this just another bug I'm supposed to live with and work around, or am I doing something wrong? My old method was to devote a separate track to pitch correction, Apply Effect, and then copy the corrected clip to my official audio track. Someone told me that was not necessary, so now I'm including Melodyne as just another effect in the track itself.

IIRC, there have been some past issues related to timing of Melodyne as a region FX. If you're still on X3e, it's possible you're running into an old one. I don't think it was generally a problem, just in specific circumstances, but I don't recall exactly. You might do some Googling against site:forum.cakewalk.com if someone else doesn't chime in.

Thanks. To be clear, this isn't a Region FX, just a regular instance in the regular old effects bin for the track.