What material is the tub made of?
The manufacturers often state in the installation instructions that bedding (supporting) the tub in mortar is optional. Personally, I think that is a major copout. The tub needs to be fully supported as it could hold say 30-60 gallons of water and maybe a couple of people, so the total weight could be over 1/2T. Most tubs will flex if not supported. If there had been leaks, it could also be the subfloor moving since it was weakened by leaks. The ledger board supporting the lip could have loosened over time and you hear that (small) movement as it rubs on something. Have to be there to tell.
I'd be tempted to poke a hole in the ceiling below (unless there is a panel you can remove to look) and see.