Called Savage today and asked about the"repair" they done and she said the tech did not specify anything. She said it was not uncommone for the reciever to be off but not enough to keep the scope from being sighted in. She said the tech did not send it to the department to check the reciever either. Savage is having UPS pick it up tomorrow.
Other info I checked.

Both sets of bases I have tried come from Savage and have S51 stamped on them. They both measure 0.222 on each end, not a base issue.
Scope on the returned gun appeared to have been tightened down on the back base and then tighened down on the front more than once. Front ring screws were not as tight as back ring screws. Guessing they pulled it down tight enough to get it sighted in. Scope they returned was not maxed out in the up but close, around 24 clicks.