Is it latency or jitter? Or is it just the start of each loop is not consistent? If it’s the latter I’d try extending the loop out side what you want to record and and see if it rights itself when it gets to the bars you want.
If it’s jitter it could be the USMAO plug-in isn’t functioning properly . I,d check by recording the click stream and compare it with the results you’re getting back in. Also test with your system set to different sample rates and see if that make a difference.
Another thing you might test is using different volumes of the click stream - I use the Innerclock SyncGen pro and you have to dial in exactly the right gain, otherwise results aren’t as expected.
Keep in mind, the MD has one of the most unstable midi clock of any drum machine ever made (~2ms jitter) so results are never going to be perfect