RonS - 5:38 am on Feb 8, 2007 (gmt 0)

Not necessarily. While there is a possibility that the two programs are unrelated and scan the source data (the payments) independently and produce either physical 1099s or electronic records, I'd imagine (and hope) that the software that creates the physical 1099s either read the file going to the IRS or created both files (the one to the IRS and the one to the printer) simultaneously.

Otherwise you open yourself up to discrepencies...

(I was in the financial industry software business... :) )