1099 Question

We converted from using a 3rd party ACH transmission package to the Sage ACH in June of 2013.  We always used the "EFT" payment method for the ACH vendors and always maintained our 1099 data in Sage 500.  We are working on 1099 processing and find that the 1099 data is has not been picked up since the conversion to Sage ACH processing.  We added "ACH" as a comment when we began using 500 to create the ACH file and all the transactions are visible in BIE - but the 1099 data has a very clean cut-off when the transactions with ACH in comments start.  Any ideas ???