Plan effective 4/1/04, with 9/30/04 PYE, so 2004 form is filed for the first plan year because it began in 2004.

Now for the 9/30/05 Plan Year, I need to file another 2004 form because that plan year began in 2004.

Will the DOL get confused (i.e., will the software program spit it out)? I'm wondering if my intitial form should be filed on a 2003 form to avoid confusion (obviously, I would indicate the appropriate plan year in the space provided).

Hmmm a dilema. You can file two forms with same year on them, just make sure you indicate the dates the return covers. This is very common when sponsors have fiscal years or change plan years.