How to reproduce problem:
I can assume, that some java code inspection feauture inside IDE performs on-fly checks, "thinks" that this code is Java class, and repaints icons inside project explorer, making this in struggle with PHP plugin. By the way, PHPStorm IDE doesn't affected by this problem.
Question itself: Does anybody know how to prevent this blinking? Maybe some hidden options to disable such "content-relating" checks, or some way to tell IDE directly that this file is PHP, not Java class and will never be :)
Pictures mentioned in p.1
Thanks for your attention
As was mentioned in comments, this is existing bug, and I have to wait for fix. Thank You chumkiu!