Ok dumb question first. are the limit switches being touched or are they away from the axis?
I am not familiar with a BDI? but if it has conection points on it for the limit switches, I would look to see if the signal is being inverted on your new BDI?
As a test you could hold in a limit switch and see if the axis error goes away to verify this?
Just my 2 cents, I could be way off.....