DTM files recording incorrectly

[Rainmaker]

If I try to record an input file on paper mario 64 (JP), it will desync within the first like 200 frames without fail. If I try another game such as melee, it works fine. I have double checked that TAS settings are on, so that's not the issue. I opened the dtm with a hex editor, and it seems as though the beginning of the file is pressing the buttons on the wrong frames (usually pressing the buttons earlier than what I did when TASing), giving the desync.  I'm not sure if this is a problem with VC games, paper mario in general, or what, but this happens around 95% of the time. Also, when playing back a dtm, it can give different results sometimes, which I'm pretty sure is never supposed to happen. Anyone know if there's something I can do to fix this?