Opps! I read your post too fast and thought it said the credits were missing in the clearing account:)

Manual cheque batch posted in AP, journal entry missing from GL. Possible causes:

1. Posting was interrupted by workstation crash, batch for GL not created. Check data integrity.
2. AP data was restored from backup after cheques were posted and before batch was retrieved to GL Transactions are stored in the subledger until retrieved.
3. Batch retrieved to GL and not posted or retrieved and deleted. (but you have already checked this)
4. Future dated or back dated transactions, in error, that are posted but just not in the period you expect to find them.