Yes Virginia TS can be a learning curve particularly when talking about A/R payments and client funds transactions.  As I can't see your specific situation, I won't make any assumptions but I will give you some things to think about that may get you out of this situation.  If you need more help, write back or engage with any of the consultants on this board.  We are always happy to provide guidance but we also provide these services on a professional basis.

First, do a backup that you are compfortable restoring from if the problem gets worse.

Second, print A/R with running balances and Funds with running balances reports to give you the client ledger for better or for worse.

Are any of the transactions you mentioned "billed" (yellow envelopes in lists).  If not, you might want to consider deleting all unbilled transactions that you can't resolve.

If you have credit transactions that are not intended as such and are unbilled delete them too.

If the remaining transactions are entered properly and the correct A/R balance is shown you should be in good shape other than to look closely at the bottom of the payment entry screens an properly apply the payments to open invoices.

Still no joy?  Get somebody to help you resolve the problem as this forum is not really intended for those specifics.

Above all else, good luck!

Thanks Allen:

After some more analysis, I realize that every time I enter a client funds transaction, it also records as an account receivable transaction.  I assume that is because the client's first payment was a straight receivable and thereafter, we drew from the client funds account.  Is there a way to get rid of the account receivable automatic entries?  I'm now cutting and pasting the bills to eliminate the account receivable info.

A payment from funds account transaction is a transaction that creates a corresponding payment against the A/R  balance and that is by design.  If there wasn't an A/R balance, you wouldn't be reducing the funds balance to pay A/R.  Something is not right if you want to disable that functionality.  Due to the sensitivity of client funds and local bar rules, I would recommend that you get somebody to take a look at your situation and train you on proper procedures.  

A payment from funds account transaction is a transaction that creates a corresponding payment against the A/R  balance and that is by design.  If there wasn't an A/R balance, you wouldn't be reducing the funds balance to pay A/R.  Something is not right if you want to disable that functionality.  Due to the sensitivity of client funds and local bar rules, I would recommend that you get somebody to take a look at your situation and train you on proper procedures.