I had something similar come up with a 990-EZ.. deleted the form and the error went away.. maybe it is some some sort of check box that is either checked or not checked. 

I seem to recall Schedule O is required, even if it is blank.

Did you get your Schedule O error resolved? I have entries on Sch O, but there is a blank line for which it wants me to enter something. I can't seem to delete the line.

Reject on a 990EZ, saying Schedule O input needs a Part and line number.  All entries have this.

Cannot get rid of efile rejections.

Sorry i haven't replied. Let me take a look at what i did last  year. It was not anything that difficult, just an oversight on my part. 

OK so what I recall is that you must scroll through all pages beginning with page 2. At the tops of the pages and dispersed throughout are check boxes that ask if you have something that needs reporting on Sch O. If you have that box checked anywhere in Proseries, it will require an entry on Sch O. You might be able to work backwards from the Sch O to figure out where the checkbox is that needs to be unchecked. If not, you must check every reference to Sch O in the return.