I don't think that has anything to do with the length of the name. My guess would be a year end discrepancy. 

I once had a nonprofit that filed on a calendar year basis for years. Then IRS changed it to a June year end in their system causing an efile reject. I straightened it out for that year, and they did it again the next year.

I'd call the eservices help desk and see what the problem is. EDIT: Or what did using that link tell you?