I don't know, which problem actually exist with your design. You reported about unintended reconfiguration when touching a connector pin. This may be surprizing, thus I tried to give an explanation of possible reasons. One was usage of a switched mode mains adapter without protective earth connection, not SMPS in general, which shouldn't cause such effects. Eletrostatic discharge is another explanation.
Apart from an explanation, JTAG debug connector contact are not intended to be touched by hand. You'll also find an Altera suggestion not to plug an USB blaster to a powered board. Considering this situation, I don't see a problem.
