Check the BPM Tempo of the song and make sure that you set the BPM of the target host software to the same before importing the tracks.

Default BPM is generally 120 for most softwares and if your song was done at a faster clip, that would explain things starting on beat 4 of bar 2. But likely only happens on wav tracks, as MIDI tracks would line up and behave off of the MIDI BPM map.


--Mac