Rob,
The problem has been identified and a solution found (and integrated in the next version of mGalaxy).
In the meantime you can use this tip:
- Open mGalaxy > Data > Definition > Emulators.xml file with a text editor
- Do a search on <Emulator name="Citra" hidden="false">, to localize the block of code
- Just below, edit this line
<System name="Nintendo 3DS" option="citra-qt.exe" script="true" cmd=""%path\%file%ext"" extensions=".3ds,.cci,.cxi"/>
to this
<System name="Nintendo 3DS" option="citra-qt.exe" script="true" cmd=" "%path\%file%ext"" extensions=".3ds,.cci,.cxi"/>
(the difference being a space added before the first """)