It seems like this issue is fixed.
Although it may need an edit? I uploaded the new firmware last night and after it did the last probe with the auto bed level it started beeping and stopped moving. It would not go to the retract position. I had to comment out the section in marlin_main.cpp
After commenting this out, it worked great and the X axis did not bottom out when it was done with the bed leveling.
So apparently my X axis was not at 15 like it expected.