The ASPA ASAP regarding the filing deadline for the 1999 5500's contains a statement that may not apply to your situation. The bar code (you know, the one you recognize as a bar code) at the bottom of the forms indicates the form, year, page number and the software provider who provided the software to you to prepare the forms. The DOL is aware of which software was able to produce fileable forms and when. It is an easy matter for the DOL or IRS to determine that the software you used was provided in time for you to have prepared all of your returns.
There was one Software provider who had great difficulty this year in providing fileable forms. If you are one of their users, I do not believe you will have a problem using the comment in the ASPA ASAP.
If you are a user of any other software provider, you may need to find a more feasible reason. Perhaps something to do with confusion because of the lack of explicit instructions, the seeming impossibility of getting the same answer twice from the IRS and the DOL or the fact that verbal instructions given over the phone for certain schedules do not match what is contained in the instructions caused you to prepare/review/research/revise/review/research/revise your forms before filing. I believe both agencies are aware of the confusion caused by the instructions and the two agencies this year. There is no need to blast them in your explanations, (Remember, Dale Carnegie, How to win friends and influence people.) but gently point out that forms that took a half hour to complete last year take much more time this year in your efforts to correctly provide the information they requested.