Groove Agent SE 5 not following Tempo Track

I’m having problems where Groove Agent works fine until the time signature changes, then it can’t seem to sync to the start of the measure. For instance, a song in 6/8, that plays fine until there is a bar of 1/4 and 8 bars of 4/4. The click track is properly tracking all of this, and I can loop the 8 bars of 4/4 and it sounds fine, but if I try to play the groove agent, it syncs to the beat but not the measure.