It is a known problem (bug 22959933) that has been fixed. We are going to make the fix available soon. If you cannot wait, please file an SR and send me the SR number.
Basically, the problem was that we switched from "where rownum <= N" to a new 12c syntax " fetch first N rows " and they apparently behave quite differently. The good news is that this syntax change only affects SPARQL queries with LIMIT.
Ok, I will check for queries without LIMIT.
The patch for the above LIMIT related performance problem is ready on MOS (support.oracle.com). To get the patch, login and search for 22959933.
Patch 22959933: Support for Apache Jena: FETCH CLAUSE CAUSING LONG DELAY GETTING RESULTS