Whatever you do, DON'T try to get rid of any Msys table. Your relationships are in an Msys table. Every database object is defined in an Msys table.
How do you think Access remembers what you have defined? Answer (rhetorically intended, of course): It writes it in one of the Msys tables.
Besides, I don't think you CAN get rid of the Msys tables. They are locked against accidental deletion. Which, in this case, is a GOOD thing. Trust me.