If anyone has the same trouble I had, it does seem simply to be that I was trying to copy the file before it was fully ready.
Since then I have been using a batch file to copy the compiled .bin across.
The following windows .bat file will first detect the pokitto, then delete firmware.bin from it and yopy testcode.bin to it. Once it is finished, it is safe to reset the pokitto. I have been doing this for the past few days without any issues at all.
@echo off set VAR=Destination for /f "skip=1" %%L in ('wmic logicaldisk where volumename^="CRP DISABLD" Get Caption') do @call :SetVar %%L echo Copying data from %Source% to %Destination% del %Destination%\firmware.bin copy testcode.bin %Destination%\firmware.bin goto :EOF :SetVar set Label=%1 if NOT [%Label%]== set %VAR%=%Label% goto :EOF