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I suppose it could be a number of things but there's probably some slight difference in the timings the games expect.  It looks like Rock Band is counting you as being late, so maybe you want to try and hit the control just before you normally would (so it'd be before the note reaches the line, I guess).

I haven't played any of these games for a while but I vaguely remember there being a setting for something like "controller lag" in one that I played and that could be the issue.  If Rock Band is delaying the response to your inputs more than the other game then it'd act as though you're playing late when you're really just playing as you're used to.

Whatever the issue, you'll probably find that if you keep at it you'll naturally get used to the new timings and it'll become second nature again.  I remember having a similar problem with a Dynasty Warriors/Samurai Warriors game once, where the controls seem the same but the slight differences throw you off.