Found a Compatability issue
 

I have found that Carbonite is having an issue with NPCScan and NPCScan Overlay.
By turning both the NPCScan addons on, Albeit the addons are older and must be forced into working in Addons options through WOW interface, but I now get a choice
Carbonite or the NPCScan/NPCScann Overlay

These break each other

will also report to the NPCScan creator

You can get most of the same NPCScan capability by installing SilverDragon instead of NPCScan while waiting for the incompatibilities between Carbonite and NPCScan to be fixed.

I like NPCScan much better than SilverDragon, but at least SilverDragon currently works with Carbonite.

I use all 3 (scan, overlay, carbonite) with no problems... what incompatability are you having?

As mentioned in the mess of notes earlier.
If I turn on NPCScan and NPCScan Overlay.
Carbonite no longer tracks Quests, and I get the issues mentioned in other posts.
Would rather have the quests at the moment

I have to agree that there's most likely another addon causing your issues. I use all three of these addons and have absolutely no problem tracking quests with Carbonite. Out of the well over 120 addons I'm using presently, none conflict with Carbonite.

I'm not sure why people would prefer NPCscan though, as 8 out of 10 times SilverDragon will alert me to a rare and NPCscan will still be out taking a whiz somewhere. I've never had NPCscan alert me to something SilverDragon didn't also alert me to. Only reason I'm using both (plus the overlay) is to test for one finding stuff another wouldn't. I'm getting ready to dump NPCscan though for it's complete lack of usefulness.

I had the same problem a while back that the original poster noted, I think around the time Rythal took over Carbonite, and I also tracked it down to a NPCScan/Carbonite incompatibility. After looking at other similar addons I settled on SilverDragon to replace NPCScan and had it installed for a week or so.

At the time I was going to post about the problem and my solution to it, but I completely forgot about it until I saw this thread today.

If NPCScan is working for Rythal and Qithe I suppose either Rythal or the author of NCPScan must have fixed things.

I ended up removing SilverDragon though as, once I thought about it, I realized that when either addon had popped up a notification of a rare I was usually involved with something else and and I just about always ignored the rare. The two addons sounded good in theory, but in practice I wasn't using them, so I guess bagging rares just isn't my cup of tea.

I suppose if I ever get the bug to go after rares again I'll probably re-install SilverDragon for a while, but I doubt if that's going to happen any time soon.

BTW, I agree with Qithe, SilverDragon is noticeably better than NPCScan.

i use Carbonite and NPCScan & Overlay with absolutely no problems!

Make sure you are using the newest beta, the .1 didnt work with NPCScan, the .2 one does!