That would be the problem I'm sure. I'm guessing it's looking for something in the Electronic Arts\BF2142 folder, but if you downloaded it off EA downloader before EA Link isn't it in a different folder?
I got something along the lines of "Patching Failed!" [Ok] "Patching Complete!" [Ok] "Patch Successfully Applied!" [Ok] and then the patcher closed. I tried running it again and I got "You've already got a more recent version." and now the game CTD's every time I try to log in.