One sided Undeposited Funds Account

Hi 

I am looking at a file where there are one-sided transactions in Undeposited Funds. I have reconciled the account and am left with about a dozen Bank Deposit transactions but there is no deposit into the undeposited funds account so it cannot be reconciled. I have tried to journal the balance out but this then puts a transaction into the Prepare Bank Deposit. 

Has anyone come across this problem before? 

If yes, how did you fix it.