Hi Shane, as far as I know the "combine same named objects" option in Moi is working properly.
But some programs that you import into decide on their own to combine objects of the same name together into the same mesh object.
If that's what you are running into then changing the setting in MoI would not look like it had any effect since the importing program is doing the combining itself at the import step.
Try looking for some option in the receiving program to turn off that combining.
To run that script set up a new keyboard shortcut and paste the script in, then you can trigger it with the shortcut key.
Also if you select all the objects with the same name and assign them a blank name that will remove the name, and objects with no name assigned to them will get labeled with separate cooked up names like "object1", "object2", etc... when you export to OBJ.
Thanks Michael, I'm using Cinema 4d so looks like it is doing the connecting. It's not a problem for me to just delete the names. I'll also give the script a go.