A similar problem is reported here: https://sourceforge.net/p/jabref/bugs/1110/ (#1110 Opening the context menu is slow for a large databases).
I use JabRef 2.10 on a 13" MacBook Pro (late 2013; 2,6 GHz Intel Core i5, 8 GB 1600 MHz DDR3) running Yosemite. My database contains 744 entries and selecting a group takes about 35 seconds to show up. But even with a slimmed version of my database with 128 entries (and 28 groups) every action takes seconds to finish. Sometimes I even have to kill the JabRef process since JabRef doesn't react anymore. Immediately after starting JabRef it's fast and everything is working fine. But then it gets worse with every minute. So I have to restart JabRef again and again. Is there a fix or workaround?
Could you provide us the .bib file? You can also send it privately.