The major issue was that in my previous database we used a given schema and that schema wasn't recreated now by DDLUtils. I've tried tweaking the ant task parameters but still nothing. I even done some quick sed scripts  to add the schema myself (rename tables from "oldname" to "schema.oldname" basically). But all this meant nothing. Plus that the database was 100MB+ and import time was well over an hour so I couldn't actually try a lot of times.
The solution resided in the Derby FAQ but it wasn't until someone from the mailing list pointed it to me that it struck me:
The current schema for any connection defaults to a schema corresponding to the user name.You see, I was creating the database beforehand with some random user like "admin". I didn't notice this was the default schema. Also, while reading the same FAQ, I just skipped to the part with SQL.
So: if you migrate to Derby, always create an username with the same name as your schema (the one you import).
1. I wouldn't actually put Derby on a production server but I feel better during development having the data in a more cross-platform DBMS . Plus, I'm spared of all the security issues MS SQL has (or at least my fear of having those ports open).
2. Yep, sed. I know some XSLT might have been smarter but I'm quite rusty at that and there is no easy xslt shell/script I could use.