(my explanation might be a little confusing so i apologize if it is)
(also, this is just how i learned to do it)
this is not related to the choppyness but the oto for the vowels are off-timing... the vowels start before the note is supposed to start
usually for samples like "u d" or "a b" and samples like that, i put the overlap, preutterance, and fixed around where the vowel ends
in the regular cv samples (other than the vowel ones), i put the overlap somewhere near the middle or start of the consonant, and i put the preutterance right when the consonant ends like usual, and then i put the fixed in different places depending on the sample
with cv samples like "びゃ" and "ぴゅ", i put the overlap near the middle or end of the consonant and the y sound, and i put the preutterance right where those two end (like i said before), along with what i said before about the fixed
i hope this helps!

(also sorry if you were wanting someone to oto your voicebank for you or something)