Off the cuff, assuming you're using RP or HILIC, but some information about your column and chromatography modes might be helpful.
Try a few pH adjustments in your MP (1 around 4.0-4.2, another around 7, and another around 8.5-9 -- column willing) and see if one of those pH ranges helps. I have a feeling the low pH might make the difference. Start with using 0.1% Ammonium Formate + 0.1% Formic Acid (1g/L in water of each) and rerun it.
Another thing, ammonium bicarbonate is inherently unstable in aqueous solution. I doubt your mobile phase is good after even 24 hours. I had problems with aqueous Ammonium Acetate's pH changing slowly over time, and the only thing we could figure was ammonia was evolving out of solution. When we changed the cation to potassium, the problem went away. (Granted we weren't using LCMS, so we could get away with using K.)
Food for thought:
Ammonium Bicarbonate -> Ammonia(g) + Carbonic Acid(aq) -> Ammonia(g) + Carbon Dioxide(g) + Water
Room temperature is enough to slowly push this reaction forward.
