Sorry for the double-post.
I tried to patch 3055 - Chrono Trigger (U)(FIX)(Xenophobia).nds with http://crackerscrap.com/index.php?p=ctds and this is what happend.
The patch changed 3055 - Chrono Trigger (U)(FIX)(Xenophobia).nds into ctdsu-ttds.nds
Then it made another ctdsu-ttds.nds that's...