I have a board using the F28M36 with two different Ethernet Phys. With the the two channel Phy I have no problems both running it through JTAG or without. For the single channel PHY I can run it fine with JTAG but if I run it through JTAG the PHY doesn't start up properly (no negotiation). Most of the lines are the same but on the single channel PHY we use GPIO's 35, 45, 54, 62, and 88 whcih we don't use on the dual channel. Do any of these lines have issues when being run through JTAG? i know GPIO35 in a TRACE line for ITM. We are not using ITM but I thought maybe this is an issue when running JTAG?