What HPLC column are you using? What reagent did you use to lower the pH? What are your source conditions and HPLC flow rate?
I think Andy's right (pun intended). I've seen this a couple times before where insoluble salts were formed when adjusting pH.
I would probably recommend having your system cleaned/PM'd if you are able to. Last time this happened, it made it all the way back to the quads.