Likely due to constantly re-building the model. Need to check procedural parts / etc to see if they handle this, and how.

Might try just deleting and recreating the highlighter whenever part model is rebuilt.

Highlighting works on a re-loaded part, or revert-to-editor part. Should definitely investigate recreating the highlighter entirely after meshes are updated.

More research -- might just need to recreate the parts' highlighter component whenever the model meshes are changed or updated.
Could be as simple as:

part.highligher = new Highlighter(part);

This is.... potentially unsolvable without some patches to stock code. It does some strange caching of the highlighter somewhere that I do not have access to. Have opened up a forum thread to see if I can get any more information / if anyone else has any knowledge about it.
http://forum.kerbalspaceprogram.com/index.php?/topic/129527-re-initialize-editor-part-highlighting/

Have finally tracked down the problem -- a private cached list of renderers stored in Part, that is only updated/initialized when the first mouse-over event is called.

Have begged NathanKell to look into fixing it, and we'll hope that such a fix or workaround becomes available with 1.1.

Have a WIP workaround, hoping to get it deployed and tested tonight; should be available with the next update. (Not a proper solution, but a hack-around like I have done with the black-body glow...less than optimal, but good enough for these purposes, esp. since it will only be active in the editor).