I do have a problem with my search in Dolphin 5 and KRunner on my Laptop. It fails to find a lot of files in my home directory which I'm able to find with Dolphin4 (albeit it takes a few seconds to find them). I tried to reset baloo completely which seemed to fix the problem at first, but it still fails to add new files.
balooctl status shows the following:

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Baloo File Indexer is running
Indexer state: Inaktiv
Indexed 132850 / 132850 files
Current size of index is 102,97 MiB

Running balooshow on a file that can't be found (.java is not in my exclude filters, it also can't find mp4, m4a, etc. files, so extensions aren't the problem):

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balooshow not.java
Keine Indexinformationen gefunden

Adding a file manually works, after that I can find them via Dolphin 5/Krunner:

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balooctl index not.java
Indexing /home/gery/not.java
File(s) indexed

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baloosearch not.java
/home/gery/not.java
Elapsed: 0.540616 msecs

I also tried to run balooctl check, but to no avail.

Running Kubuntu 15.10 with baloo 5.15.0.

I'm having the same problem as are others. See here: https://bbs.archlinux.org/viewtopic.php?id=206445. I didn't bother deleting everything forcing it to re-index since that was obviously not going to solve the underlying issue that baloo is not indexing new content.