You need to free the space on rootfs. I've just tested on my N900 and stratagus runs fine with the data in /home/user/MyDocs/games/stratagus instead of /media/mmc1/games/stratagus, so I'd suggest moving the data back there. I don't know why this was failing for you before - it gives me a few errors about missing files (sound files from the looks of it) but that doesn't stop it running (I get the same errors with the data on the memory card).

As for editing the files, doing so with a Windows editor can cause problems as that uses different line endings that Linux does. You'll need to make sure that whatever editor you use is capable of recognising and saving UNIX format files.