Today I downloaded and installed the most current version of the software on Epson's support site. I believe this was different that where I was instructed to download the software in the scanner packaging materials.
The numbering seems to be correct now, i was not skipping numbers based on whether there was a back scan that was saved.
I did notice one anomaly still, when starting a batch you are asked for 3 pieces of information which is used in creating the filename. A year choice (or year range) a season or a month choice and a custom description. The first two are popup menu choices, but there is a "empty" menu choice to exclude them. However when I left the custom field blank, the scanner operated using a sequential number that was not reset between scan jobs or batches, so each folder would begin with the next number after the preceding batch. A little odd, I would rather it always start with 1. Including a name seemed to resolve the problem, so I left the month season choice blank and put that into the custom field. I may choose to use a custom field and not bother with the popups anymore.