I had about this same thing happen I made a stand along uno and it works great I put it up and about a year later I see it and I think what the heck let's add it's own usb to serial and I did the dang thing pops up it can't be programmed.
Now what the heck It worked and all I did was nothing but a hook up a usb to serial.
Well after about 4 hours looking at this thing I found the problem I put a crystal on it and like I said it worked well the leg is broke on the crystal it now works when you press down on the crystal.
I fixed that it now works all the time but somethings are hard to find.
Bread boards pins can also get bad over time most time you remake it and it will work agin as it did before.