I, too, have encountered this problem and would love to see it fixed.
The standard Blizz map has no problems with Total RP, however, it is distinctly lacking in the hover-mouse-to-switch-zone department.
Furthermore, if you try to set a goto in another zone using the map like this, Carbonite assumes it is a part of your current zone and tries to send you back into it if you decide to leave for the new zone.
I've posted a comment regarding this on the Total RP download page as well (
http://wow.curse.com/downloads/wow-a.../total-rp.aspx ), hopefully either of these two outstandingly brilliant programmers can find a solution.
Edit: Upon further inspection, the standard Blizz map seems to have a problem as well. This occurs even when Carbonite isn't loaded, which would mean the fault is entirely Total RP's.