We switched from Acetonitrile to MeOH and it works like a charm. So it seems like the problem was that when the aqueous mobile phase with 50 mM Ammonium Formate came in contact with the ACN mobile phase, the salt would come out of solution and we had a mess of a situation. With MeOH this does not happen.
I guess with the Symmetry column we got away with it a little better as the analyte was more retained at the beginning of the analysis when this "desalting" was occurring.
It is true our mobile phase has no buffering capacity. But I have always thought buffering capacity was overrated (unless you are very close to the pKa of the analyte - which is not a good way to do things anyway). I like to keep things simple. Unless you are concerned that your colleagues will be putting acids and bases in you LC system while you're not looking, I don't think buffering is critical. I have used these kinds of mobile phases many times in the past and they generally work fine.
Now I will sit back and await the avalanche of hate mail that I know is coming in regards to my latter statement.
You won't get any hate mail from me. I would tend to agree with you. I will use a buffered mobile phase when the chromatography demands it and not before. 90% of my analyses are performed using 0.1% formic acid in H2O and either ACN or MEOH.