I have my single loop songs set up on manager as the intro and then a soundless loop as the main for one click goodness to do the entire song. I tried it in reverse with the song loop in the outro slot and the "no sound loop in the main. I found that I preferred the main loop in the intro so switched them all back. But now, when I load the project into the BBP some of the songs main loops are still showing up as the outro. Befuddlement ensues.
Have you synchronized your project with your SD card (or exported it)? If something doesn’t seem 100% right, let me know and we can set up a phone support session. From what you described, I cannot completely tell what’s happening on your end, so it may be a good idea. PM me if you’d like to set up a session like this. 
I saved project and synchronized to card. That’s when I had the issues. After posting, I saved project as… and reloaded it to card. Now it works. Not sure I could explain or reproduce the problem. I’ll pay closer attention and if it happens again, I’ll be better prepared to go through it with you. It was strange.
Okay, keep me updated. Thank you.