Sounds like garbage collection
You could try changing the settings in your eclipse.ini, maybe with a higher Xmx value
--launcher.XXMaxPermSize
256m
-vmargs
-Xms256m
-Xmx1024m
-XX:PermSize=64m
-Xss1M
-server
-XX:+DoEscapeAnalysis
-XX:+UseConcMarkSweepGC