I think I had that problem wayyyyy back on like FL studio 7 or something around that. I think my work around (because I never found the answer to this) was that after I was done with sequencing everything to perfection in song mode I would select all the patterns in the song window and drag them a little bit to the right so that way the beginning that would normally be cut off would not matter because I moved the patterns back a little bit to start at a later time. It might have something to do with the buffer latency maybe?
I'm using a different program to sequence now so unfortunately I wouldn't be able to try and recreate your situation. Good luck.
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