From my own local tests, if you have that houdini.env with our values in, and launch Houdini through Shotgun Desktop, both will work. Do you have the shotgun toolkit installed differently or using it differently?
There might be an issue with us just straight up overriding a value that Shotgun is setting somewhere else, so one thing you could try is to modify those two values to look like this (with the paths you’ve specified instead of “[HOU SUBMITTER DIR]”):
Looking at the Houdini docs, the reason the ampersand, &, isn’t working seems to be because it only adds the ‘default’ path for that variable.
Thus, if Shotgun is modifying that variable (HOUDINI_PATH), it obviously wouldn’t be in the default paths, thus we were probably overriding it if they were setting it before us.
You could always compare the two Houdini environments if you’re curious. Once again from their docs, if you use the hconfig.exe you can use this to see the difference with and without the $HOUDINI_PATH/$HOUDINI_MENU_PATH string.