1-Instead of routing thru buses to AUDIO tracks, just use Commit up to This Plugin and see if that helps.
2-Show Delay Compensation and you may find some tracks where plugin latency is affecting timing.
3-Worst case, since you can see the offset, use Tab to Transient to locate the start of audio, separate the clip and nudge the audio back to line up(you can do this on a sample-accurate basis, but close is likely going to sound fine). If you check several and discover that all are late by the same amount of samples, then its simple to nudge by that amount
