If you try using the Geany.lnk created by the installer in a batch script, it overrides the current directory to the install location. It would be better to leave "Start in" blank so that e.g. creating an alias to start geany:
doskey jot="c:\Program Files (x86)\Geany\Geany.lnk" $*
works as expected.
The "start in" directory is set implicitly by the installer when it created the shortcuts.
Attached is a modified version of the installer which does not set the directory in the created shortcuts.
Could you please test it and provide feedback whether this solves the problem and has no other side effects? I didn't really test it.
And please be aware, that the installer is built from GIT master which is way newer than the 1.24 release.
Thanks.
Attached is the patch I used for the installer above. I still would like to wait for feedback and/or other testers before committing.