If the customer ledger is higher than the BS, I would suggest it is because there is a transaction in the sales or deposits that debits and credits the A/R GL account.  For example is you start off with a balance in the customer ledger and the general ledger of $100.00. In the next month you create a transaction to the customer for $50.00 but you choose the same A/R account rather than a sale account, the customer ledger would show $150.00, but the BS would only show $100.00.  To find that transaction you need to run the Sales Journal Report for the dates in question. Under the account ID column look for an entry that goes to the same A/R account.  If you can't find it in the Sales Journal Report, try the Cash Receipts Journal Report.

It is possible that a general ledger journal entry was made to the A/R account directly affecting the general ledger which does not post back to the customer ledger. You can run a general ledger report for the A/R account for that month, look at the column JRNL to see if there are entries with GEN (a general ledger journal entry) and investigate why they were made.

Set up a due to xyz company (Liability) in one company and a due from abc (Asset) in the other.  Use those accounts to balance the two. 

Thank you for the responses!  We finally got it figured out!  Turns out that we originally had a Credit Memo, but no Invoice to offset said Credit Memo.  We were on the right track, but didn't get it all the way through.