This should not happen. Ideally you should be able to find an adjustment for the v-hold pot that covers the required "arcade" range, roughly 50-61Hz. If you can't achieve that, first check whether the desktop's mode actually locks or only looks like it's locked (veeeeery slow roll), this would point to an issue with the vertical sync signal. If you're positive that it's locked, then find what's the actual refresh range your monitor can handle. Write down refresh rates instead of games that work or not, and see if there's a correlation and we can use it to build a crt_range that avoids the offending values.