I had something similar happen to me and I had to call Aquarite to get it straightened out.
When I started the pool up last year, I was getting really high salt readings and as a result the system would not generate chlorine. After calling Aquarite, they walked me through the control panel settings and figured out that the control unit was not set for a t15 cell (I don't know how it changed). The system will generate different salt readings if there is a mismatch between the cell you are using and what is programmed into the control unit. I'm not sure why it would make a difference in a salt reading, but it does. That said, once the control unit was set back to a T15 cell, the readings were in line with what I was measuring and what the pool store came up with. Everything worked fine after that.
I would recommend calling Aquarite, if you can't get it resolved.
Good luck.