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Join nowTwo strikes against you already - one for putting a CC account in as an AP vendor, second for using JE to make AP entries - both are NoNos. Stop doing this - the CC system on its own works fine.
To fix your problem my guess is that there are 'unapplied' offsetting items in the CCvendor. Open PayBills, select that vendor, sselect any unpaid bills then 'apply credits'