I had my bathroom and shower installed about two years ago. There was a calcium buildup on a number of the grout lines on the shower floor. I removed the calcium deposits, installed new grout and for some reason the grout will not dry. Is it possible that the mason did not install enough of a mud base and water has found its way between the mud base and liner installed under the mud base? It is obvious to me that something is not right with the installation. I don't want to seal this shower until I know what the cause is. Please advise, thank you.

Your new grout is defective or improperly mixed. Good grout will dry rock hard under water. Do not seal this, remove it completely and buy new powdered grout, avoid premixed in a can.