Unable to JTAG MEGA2560 R3

Question

I am getting the same error I see others have had using a brand new install of "Microchip" Studio 7, with the MKII programmer. I am trying to program a Arduinoish Mega2560 r3 board. If I go into programming using the mkii ISP cable to the r3, I can read voltage, and if I hold down the reset button on the r3, and time it just right, I can read the ID. Otherwise, I just get the fail others have seen saying unable to enter programming mode. What I really want to do is set the JTAGEN fuse so I can use JTAG. But that has the same/similar problem. I can sometimes read the fuses by holding the reset button down and timing it right. JTAGEN and OCD are NOT set. I can get the board(S) (I have multiple with same issue) to program flash with AS7 using the USB cable and avrdude based "external tool". But that is really just using avrdude. It is unclear to me why the mkii connected to the 6pin ISP port, and setup as ISP in the gui, is broken. I can only get it to read using the mkii, with some combination of holding the reset on the r3, and hitting the AS7 gui read button just right. Any suggestions?