We have seen several cases when customers upgrade to GP 10.0 or GP 2010 where EFT computer check batches in Payables Management are going to Batch Recovery and seem to get caught in a loop. When you free up the batch and view the Edit List, the error message says "Duplicate check numbers are not allowed".   The two most common reasons why this happens are:

1.  If the Next EFT Payment Number in the EFT Payables Options window in the checkbook (Cards|Financial|Checkbook|EFT Bank|Payables Options) is set to start with the prefix 'REMIT', this can cause issues with zero-dollar check remittances.  The prefix 'REMIT' was used in the past and so this causes a duplicate check number if you started the number lower than the last used number.  Also, the system still uses the 'REMIT' prefix for automatically applied documents, so it could interfere with that process too.  Therefore we suggest starting the Next EFT Payment Number with the prefix "EFT" instead of 'REMIT" so you don't run into any of these issues. For example, change the Next EFT Payment Number from REMIT000000000004003 to EFT00000000000004003 instead. 

2.  Another reason for this message is that the user is sorting the checks by NAME during the checkrun process, using functionality in a 3rd party software.  To get around this issue, we suggest to leave the default sort for the checkrun, and contact that 3rd party for further assistance to get any check sorting functionality they provide to work without error.

I hope this has been helpful information to you.

Cheryl W.