Tried the following as well. The game launches but the value of fs_game is still not set to mods/bots.
set gamepath=%cd% set mod=mods/bots cd /D %LOCALAPPDATA%\Plutonium start /wait /abovenormal bin\plutonium-bootstrapper-win32.exe iw5mp %gamepath% -lan +name "phase19" -fs_game "%mod%"