I can't replicate your problem either -- it just sits in the tray when run from Explorer.
It's not in fact possible to start StrokeIt minimised as the window isn't minimisable. The window just opens as normal.
For reference, start minimised can be invoked as follows, for programs whose initial window can be minimised:
start "any old rubbish" /min some_program.exe
The first argument, window title, appears to be mandatory but useless here. (It's not required but, if omitted, opens a command window whose title is the program you were trying to run ;-)
Type start /? at the command prompt for full details on this gnarly and particularly obstinate command.