Sounds okay to me - I'm not detecting any difference in speed between the two (for the few tracks I've sampled at least). Is the problem isolated to a few specific tracks or is it global in scope? Also, are you comparing the two with the same player, because some HES players (particulary NEZplug) can have some strange timing problems at times.
What I'm seeing in the HES (timing-related $E0D8 calls):
LDA #$02 , STA $F8, LDA #$02, STA $FF, JSR $E0D8 (60 Hz base timer)
LDA #$00 , STA $F8, LDA #$00, STA $FF, JSR $E0D8 (use TIQ)
LDA #$2A , STA $F8, LDA #$0A, STA $FF, JSR $E0D8 (use timer index #$2A, which sets $0C00 to #$68)
As far as I can tell, the tempo isn't ever set by the music data itself so I expect $0C00 to be invariant over all the tracks.
Just to check that I'm hearing things ok, I've also checked $0C00 in-game with a sampling of music and I also find it to be #$68. I also verified that the music is indeed driven by TIQ by changing the timer value in a save-state and reloading (the music tempo changed as expected).