Welcome to the forum, Coati. Are you writing microtonal accidentals for transposing instruments, and showing the score in e.g. concert pitch and the parts in transposed pitch? If so, that is probably the nature of the problem. You can search some of the other posts on the forum for the details, but it comes down to the specific combination of divisions required for a particular accidental not being precisely the same when you add a certain number of 12-EDO divisions to the pitch to account for the instrument transposition.