I have indeed tested the latest master version from http://builds.jabref.org/master/ and the problem persists.

Version: Jabref 4.1 on Windows 7 on Java x64 Version 8 Update 162

Steps to reproduce:

1. Use large datebase (>1800 entries) with almost every entry having an associated PDF
2. Type something like "author = M"
3. Randomly observe that the searchbox will suddenly show "author=Mauthor=M". This does not happen every time, but on our system it takes about
   
4. The search will be largely broken afterwards

The only way to fix this is restarting Jabref.