I think I stumbled onto the problem and fixed it....completely by accident.

When I encountered the issue I described above, I had only completed the song chord sheet through the intro, verse, chorus and a turnaround going into the 2nd verse. So the complete song chart wasn't there....I hit play to see if it was working, and got the error I described.

On a whim, I went ahead and completed the song chart, thinking that if somebody gave me the solution, I could implement it and the song would be done. After inputing all the changes until the very end, I hit play and bam...fixed.
Played it correctly including the 2/4 bars everywhere they occurred.

So my guess is that the real drums don't "reset", for lack of a better term, until you have an entire song chart laid out.
Certainly not an error or issue, but an interesting quirk to tuck away and keep in mind.

http://www.rogerbrownsongs.com
http://www.nashvillesongwriters.com/roger-brown