Many features in Visual Assist related to coloring and highlighting, e.g. Highlight References to Symbol Under Cursor, require parsers that look ahead at code being edited. The parsers apply color and highlights to code not yet visible so when the code is scrolled into view, the colors and highlights are immediately visible.
If you have outlined code or regions that contain large blocks of code and collapse those blocks, colors and highlights beyond the blocks may not be visible if the parsers in Visual Assist did not look far enough prior to the collapse. If this happens when you collapse code, you can increase the number of lines the parsers look by adjusting the following entry in the registry:
HKCU\Software\Whole Tomato\Visual Assist X\<IDE spec>\MaximumScreenReparseLineCount
Default value is 300.