This is odd I have not seen this happen in GP. How are you populating the data? Are you allowing duplicate transaction numbers in the module? None of these duplicates are voids?
2 things I would try to correct the problem (in a test database first preferably)
1. Run check links on the RM Transaction Open and History tables?
2. Run AR reconcile on the customer,
Don't forget to back up in case you need to restore your data.