This is a common problem when monitoring multiple sites on the same system. The problem is worse when one or more sites yield less than perfect reception. mpdonala is probably "jumping" from one site to the next. Calls from the new site pollute the previous site's data - in this case with channels. After a few seconds (or minutes) the program figures out the site has changed and switches over to the new site. At 100% decode the program will usually back out any erroneous additions.
If a control channel is red (active) on one site and brown (alternate) on the other site, the brown channel needs to be deleted. If you see more than four control channels total on a Motorola site - something's wrong. You will want to figure out which channels don't belong.
Once you get your bandpland figured out - you'll want to do two things.
1. delete the HZ file (again) - the program will use the band plan to re-populate the channels with the correct frequencies.
2. when switching sites - exit the program - tune to the new site - restart the program.
That should clean out any crud in your channel list and prevent future problems.
With that said ... try a base of 406.1125 and an offset of 380 - for all three sites. You will want to verify each voice channel to make sure the calculated frequency matches reality.