When embedding JS inside a HTML document the background colour flicks between the configured colour and white. Simply clicking in the area will cause strange behaviour where the colorisation ends up mixed between white and (default) green.
The syntax colorisation of the JS is not affected, just the background.
*** Bug 230274 has been marked as a duplicate of this bug. ***
This is IMO caused by some bug in the highlighting layer. Possibly related to Bug 225341 - Syntax highlighting in JSP occasionally stops working
This is working for me now in:
Product Version: NetBeans IDE Dev (Build 201308270854)
Updates: Updates available
Java: 1.7.0_40; Java HotSpot(TM) 64-Bit Server VM 24.0-b55
Runtime: Java(TM) SE Runtime Environment 1.7.0_40-b40
System: Windows 7 version 6.1 running on amd64; Cp1252; en_US (nb)
I do see a minor problem still with some green highlighting appear on the white space before the ending script tag, that is not there in earlier versions. But it goes away if you click on the editor above the ending script tag.