Yeah, I didn't think that would fix it but it was worth a shot. It sounds like it's just confusing the synth when it hits the loop points. I'd try to set the loop points in between MIDI notes or if that's not possible temporarily muting any notes that surround the loop points.
Oh and maybe increasing your buffers would help if you are just mixing or if you are recording using a lighter synth to capture the part then switching it over to the one you want afterward.
IDK... just tossing out ideas.
Cheers.