The "Start in:" field in the Geanly.lnk should be empty, it's currently set to the install dir and this prevents command-line invocations from opening relative-pathed file arguments correctly.
Also it would be useful for scripting/debug to have a mode where geany stays attached to the launch cmd console (`start "" /B /WAIT "C:\Program Files (x86)\Geany\bin\Geany.exe"` is a possible work-around) --- Reply to this email directly or view it on GitHub: https://github.com/geany/geany/issues/786
