The batch file doesn't work since the application searches for the files inside user's name when a shortcut is created.
A workaround I found goes like this~
(i) copy the the target field's of PokeMMO and GEC, in your case
start "" "D:\PokeMMO\PokeMMO.exe"
start "" "D:\PokeMMO\data\mods\Gilans Encounter Counter\GEC\GEC.exe"
(ii) Then just save the notepad as 'name.bat' and SAVE it in either the folder which has the GEC app or the debug folder in the GEC Mod's Folder. It seems to work for me in either of those two folders.
(iii) Then you can just create a shortcut of that bat file and move it anywhere ya like and it'll open both the apps. If you wanna pin it to the taskbar or start menu, just open the target field by clicking properties of the bat file which is not the shortcut(aka name.bat here) and type '/cmd c' in the beginning and you'll be able to pin it.