When I try to switch from a fill to a beat in perform mode the first beat always gets cut off. This doesn't happen in any of the pre-programmed beats, or in compose mode, so it can't be normal. Any thoughts on why this may be happening? Thank you in advance.

Do you mean when you are in one of your user patterns and you switch from, say A to B using a fill? The only thing I can think of is that when you recorded your pattern you may not have quantized and came in too early on the downbeat, which could cause it to be "lost" on the first bar of the pattern. Otherwise, I'm not sure what you mean, because you can't really stay on a fill for more than the duration of the fill, then it will go to the alternate pattern or, if you hold the fill button down through the downbeat, it will go back to the start pattern.