My guess is that the "file naming" rules are set (new in ST9 with the BiDM). Try setting to "none" as shown as it works for me and mine is set to none.
Is this only happening when you save as a flat? I had a similar issue when I attempted any "save as", My options were grayed out and nobody could find a reason why. This happened to be while I was SEU this year, and I spoke to quite a few people. This was only on my laptop though, desktop was ok and both had MP installed sametime, or maybe it was the ST9 update. Either way I had to reinstall for the grayed out issue to be resolved. Hopefully it's somehting simpler for you?
Do you know which line it would be in the options.xml file? I see that Linear Revisions is set to NO for override and FALSE for value. Or might it be one of the options below?
Thanks for the tip on using SEAdmin. I got it! I had to edit the File Naming Rule Overide = Yes and Value = None.