syntax highlighting takes long time to show up

Hi Intellij Community,
Recently after start Intellij or checkout different git branch, my Intellij fail to highlight the syntax. It just shows plain text with basic java syntax highlighting such as void or public. It takes up to 1 hour to back to normal syntax highlighting, such as typo, syntax error and classes. This happens after I update Intellij to 2016.3.3 and JDK. I downgraded to 2016.3.2 and it did not help. I checked power save mode, plugins and preferences->Editor->Code style, file types, color and fonts. There are no abnormal settings. I also tried to disable all plug ins, still no help. Does anyone have same problem or know what could be the reason?