From what I see, paintball is in /var/ball2/paintball2. I hope this works:
cd /var/ball2/paintball2
./paintball2 +set dedicated 1 +exec config.cfg +map midnight
You want run paintball, not the folder.
edit: wait, is the paintball2 file in ball2, or is the paintball2 folder in ball2? That's where I'm getting lost.