Hi Richard,
I ran into a customer had exactly problem you described here. Here are some steps that I tried to fix the problem:
a). Check UPR30100 to remove all the dups
b). Check UPR30300 to remove all the dups
c). Run the reconcile to update UPR30301
d). Run the Quarter end (it uses uprCrossCompanySummRptsTemp table I think it collects data from UPR30301)
e). If they are using CM, you need to remove the dup in CM20200 as well, before you remove those records, you need to get the sum of those records
f). You need to adjust the check book with the amount you got from step e in Cash Account Balance CM00100.
g). Run the check links on CM Transaction
h). Check reconcile bank statement for the check to make sure there is no dup
I hope above steps will get your issue resolved & good luck.
Rob