Did you remove the saddle from the bridge? If so, maybe the edge that fits into the bridge is not perfectly flat anymore and therefore isn't making good contact with the guitar.
take the guitar to a music store and fit a new saddle to the bridge, one that fits snubly but not so snug as to crack the bridge. Saddles are very cheap and they come in various thicknesses, lengths and depths (gee those plurals look stupid, don't they?)
If fitting the saddle right doesn't help, send me a P.M. I'll ask Paul Geremia, the man really LOVES guitars and he's always fixing up something on one of his friends instruments. He got my old Martin D-28 sounding better than it ever had before simply by using an automobile distribitor "feeler guage" and a mirror to find loose fitting struts and braces. and re-glued them properly.

If you filed the saddle while it was on the bridge, the hard vibrations without a string going through the bridge plate may have jarred the bridge plate slightly loose.+ The bridge plate is a flat piece of hardwood that fits underneath the guitar top, and opposite the bridge. The pin holes go through the bridge, top and bridge plate. the ball end of the guitar string goes into the hole, down through the bridge plate and tucks under the hardwood bridge plate. The bridge pins only keep the ball end of the string tuckd under the bridge plate. There is no strain on the pin, in fact, the string 's tension holds the bridge in place by using the bridge and bridge plate as a parallel clamp. The bridge and bridge plate do need to be glued down tightly because there is "sliding-like" pressure towards the guitar neck.

There is nothing "mysterious" about guitar construction, and all you characters who told this guy to "take it to an expert repair man" , from me to you GO PISS UP A ROPE. If female this is very difficult to do,so you'd better consult with an expert.

Paddy, let me know if my suggestion about replacing the saddle works by sending me a PM and cutting out all the "experts" If it doesn't work I'll put you in touch with Paul.

Oh Lord, protect me from expert technical phraseologists. I KNEW WHAT HE MEANT BY "THINGAMAJIG" WHY CAN'T YOU JUST GIVE HIM THE RIGHT WORD WITHOUT BEING SNOTTY ABOUT IT? fOR GOD'S SAKE, YOU GUYS ARE ACTING JUST LIKE PARISIENE FRENCHMEN. AND I DON'T GIVE A RAT'S ASS IF I SPELLED THAT WRONG.