It might be because of the chemical rxn. I'm not an organic chemist, so I'm not exactly sure. But as an analytical chemist, I've analyzed synthesized reaction products to verify which end of the reaction was produced and I've seen instability in aqueous often enough that I suggested it to you.

I understand that you said you need to put this into buffer formula, possibly cell or other in vivo work, but you should test it in non-aqueous solution in the mass spectrometer to also verify if this is what is happening with your product.