there is not much I can share (yet) but:
the impact/xps download to ML300 freezes some times, problem has been fixed by restarting rebooting, sometimes pressing the "fpga prog" button.
the fpga prog button I guess simply forces the fpga to not-init state waiting for config, as sysace is not reset, it stays in non-configured state until you configure with impact.
there are no settings on ML300 that could prevent the jtag re-config it should always work (but does not)
in my case I had started v2pdk shells, debug server debugger, killed them and then tryied impact, and was freeting, not sure why.
antti