Lucene search unusable, indexing not working after upgrade to 4.1.3 (tomcat related?)

The search engine builds the index forever and thus is completely useless at the moment. This worked well in 3.5.x.

After setting the debug, the log is full with lines:
DEBUG c.x.x.p.l.IndexUpdater - failed to acquire lock, retrying in 534ms ...

Have tried to set different paths to configuration but nothing seems to help.