Have you been able to resolve?

I recently came across this same issue.

I researched to see when the issue started and pinpointed the first transaction that caused the issue by pulling a report monthly, then daily once I saw the first month that had the issue.

In the first report that showed the day with the unbalance, I drilled down into the transactions to see how credits were applied and found that some journal entry transactions applied to the credit memo, while others did not.

The next step I took was to look at the individual transactions related to the credit memo, which of course was the credit memo itself and in my case, Journal Entries that were applied to the credit memo.

I noticed that the journal entries that did not contain the Accounts Receivable at the first line in the JE would not get recognized in the credit memo, the JE that had AR in the first line did get applied correctly.

The step I took to see if the issue lies in how the JE is entered, I moved AR to line 1 as a Debit and the Sales (in this case) in line 2 as a credit. Doing this will remove any related transactions, so you have to go to Fix Unapplied Invoices to reapply the journal amount to the invoices and credit memos. After fixing the unapplied invoice, I checked the Cash basis report for that day and the balance sheet in cash basis balanced. 

CONCLUSION: It seems that the manner in which you enter JE into QB affects whether or not it can properly process the credit memo when you apply JE transaction to the credit memo.

Let me know if this turns out to be the same situation for you and if taking these steps resolves your report issue in Cash Basis.