Lpc2000

I now have a board that has seperate connections for both JTAG ports
(primary, secondary). I am experiencing the following problem. 

In warning, this one may be a problem with the NOHAU debugger!

I am required to enter the debugging mode using the Primary JTAG port,
then while connected, switch the header to the Secondary port, and
deselect debug mode, then Force a [Stop] on the debugger, then
reset(software), and everything works fine.

If I try to connect directly to the secondary port, all the correct
signals are present on the JTAG pins, but the part will not respond.

Has anyone else seen anything with this?