I have a T/C pro hunter in 25-06 and I went to check my barrels extractor engaugement on a handloaded case. The loaded case falls right into the grove tip on the case after insertion and is properly supported. Closing the action and re-opening the case is lifted up as it should.

My common sense says you have the wrong extractor in your rifle.
Check your extractor, it should have a raised tip to fit into the grove of the case.

Your have the first 25-06 barrel I have read with accuracy issues. T/C's 25 caliber barrels IMO are scary accurate. I do re-bed my forearms with a Bellm 1X hinge pin installed in my centerfire barrels. I do re-call I had to shoot over 120 rounds in the barrel to smooth out the lands and clean up was much easier.

Doc