Sounds like a classic case of rectification. Look for corroded metal to metal
contacts, both on the tower/antenna system, as well as down low, anywhere
within the near-field of the repeater..... It will drive you nuts, as I have
been through the same ordeal. It ended up being some scrap metal on the
ground that had touched some other metal, in one case... Another situation
came from my 2m duplexors sitting on a metal painted floor and making
intermittent contact... I put a board under the duplexors and that completely
cleared things up...
In a worst case scenario, II remember a western MA repeater owner's story
some years back where he would have radio WLS or some other
megawatt-clear-channel broadcaster come through his repeater at night, in
addition to the scratchies, due to a rectification problem on the site, due
to a metal to metal contact corrosion. That can be a real problem, and no two
situations are alike. It is going to be a chore finding it, if you ever do...
Good luck... 73, de Gary, W7NTF