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Undeposited Funds issue

We have daily journal entries from third party software to record sales.  The balance goes to Undeposited Funds, and then I go in and record the deposit after making sure the amounts received by the bank match.  There are generally two credits into the bank account for every JE, thus I can't just use the "match" feature but have to manually make sure the amounts are correct and add up to the total in the JE.  Each JE appears in the "Included in this deposit" list.   However, I have two journal entries, which look exactly the same as every other journal entry, that won't show up on the deposit list so that I can select them for deposit.  Any thoughts on why this would be, or a work around?  I thought I could just JE the funds from Undeposited to Checking, but now negative deposits are showing up on my deposit list.  I've spent way to much time on this silly little issue!!