I went through the same thing the first time I had an engine reset before I had the full DCS. We reset it, but then it was on the layout and got added back into the DCS.
The second time we did it right and it worked.
I've tested a number of DCS engines by doing a factory reset to them with the full DCS, then running them with the DCS Remote Commander. All have worked fine after a proper factory reset and immediately powering down and disconnecting the TIU. Every one runs with the DCSRC until I add them to the DCS again.