GL not automatically applying payments

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I was trying to reconcile the Aged Payables to our General Ledger account and I noticed we were off by quite a bit. Then I noticed that there were transactions that didn't show up in the aged payables indicating that they had been paid but they only showed a credit or debit to the general ledger. When I found the check that they had been paid with I noticed that even though the journal showed them going to the correct account, they didn't show up in the GL report. I found that re-saving the check fixed it but I've got about a year's worth of transactions that need reconciling. Is there any way to get the system to go through and automatically apply this or is it just a software glitch?