Ah, excellent tip Gyathaar!
Basically, it appears that when Pitboss starts if you choose a mod not already loaded (the loaded mod will be the default selection), it restarts and doesn't carry through the /altroot parameter.
I tried setting the mod= parameter, but nothing I did could get it to be recognized. I tried quotes, no quotes, double quotes, prefixing Mods\ to the directory, pretty much every variation I could think of and a few google suggested.
I ended up setting it in the shortcut I use to call Pitboss. After my /altroot, I added this: mod="\"Mods\Desert War\"" (I got that from the Pitboss command window - not sure if all the double quotes are actually needed)
Anyway, thanks for the tip Gyathaar. It was exactly what I needed to get moving foward.