Hey Peter,
I warm my neck up with a few licks, before I tune it, and at the end of the sets. You can see that here, we used that as the tip of the week when I dropped by to meet Andy Gurley at East Nashville School of Music.

http://youtu.be/JZIHVYEX7Jk

I get better results doing this, and you might too. There's also a couple of other things that could be happening too. It can make a difference if you're playing with a steel player, and as Razbo said it would be best to have an electronic tuner. Another thing could be that it's not you that's out of tune.

If you're sure the intonation is set correctly, and that it's not a fretting problem. You said that a guy repolished the frets, but did he redress them, and recrown them. Your intonation can also vary depending on the bridge, and I would definitely use an electronic tuner to set it. You also want to set your toggle switch to the neck pickup for the best results.

I really don't think it would be the amp, so check out some of this other stuff, and let us know how it turns out.