I've sadly been struggling with this for a while, but whenever I select text with my mouse in Aquamacs, it automatically highlights the end of the region and will continue to highlight anything typed after it, until I select somewhere else.
Kinda a minor, but very annoying issue...
possibly due to stuck Option/Alt (Meta) key
perhaps related problem that I have, is difficulty in copying region using M-w. if I hold Meta by itself for too long before hitting w, it goes into highlight mode, and doesn't "copy" the text..