jtashaffer.
So far you have briefly described in words how the system manifest itself. In order to troubleshoot anything, EXACT information is needed about what you have. If you post on a forum for help it is prudent to provide as much as this information up front in the first post. We should not have to pry this information from you.
The information I am asking about is for example: Exact type numbers for ALL the equipment in question (not just "Contrologix" or "micromaster"). Physical network details, cable lengths, terminations... Network settings, such as baudrate, busprofile... EXACT error codes on all the devices in question.
I have a feeling that this is simply way over your head. No offense.
Profibus problems can be hard to pinpoint. On top of that, since it is put together by diverse manufacturers equipment, it is even more difficult to get into. You have to know profibus, and you have to know how to program the profibus master (SST card in the Controllogix rack ?), as well as all the profibus slaves.
Someone has put this system together. Contact that person or company and get them to help.