Ok, I figured out how to fix mine, hopefully it will help you guys out.
First try this (I didn't do it this way, but it may work):
Go into the properties of the FS shortcut. Change the "Start in" to this: "C:\Program Files\Electronic Arts\Battlefield 2142"
If that doesn't work, try this (This is how I did it and I know it works):
My problem was that, after following Adultswim's directions, a 'Firststrike' folder was not created. So, follow his directions, cut and paste the Firststrike folder out of your created 'mods' folder and into the first 'mods' folder containg 'bf2142' and your 'mods'. Delete your 'mods'. Now, go into the properties of the FS shortcut. Change the "Start in" to this: "C:\Program Files\Electronic Arts\Battlefield 2142" I figured this out by looking at another mod for BF2. It works!!