Do you know autoit script ?
mGalaxy can search a script called mGalaxy_Script.exe and load it instead of the executable. So for an application that don't need script try something like that.
;Parsing
Local $count = StringInStr($CmdLineRaw, ".exe", 0, 1, 1)
local $app = StringLeft ( $CmdLineRaw, $count + 4 )
local $command = StringTrimLeft( $CmdLineRaw, $count + 4 )
if not $command then exit 0
RunWait(@ComSpec & " /C " & "start.bat", "", @SW_HIDE)
Runwait ( '"' & $app & '" ' & $command )
RunWait(@ComSpec & " /C " & "End.bat", "", @SW_HIDE)
Exit 0
This code wait for application (in bat file) finish so IDK what is your bat file but perhaps "Run" will be better.