I have/had similar experience with my new addition. On inspection he looked fine, but after about 10 days I've found small black things under his scales not a lot maybe 3 little specs.

After about another week so let's say 3 weeks I've seen these little bugger crawling over my lil baby.

I went bonkers, threw everything out, bought new box, hides, water bowl and everything. I'm using BioKill on the box itself and surroundings, it's basically the same as NIX solution based on permethrin and water. But it's widely available in all stores.

You should check the thread that was about my snake, and search forum for any other mite threads.
Here's mine: http://ball-pythons.net/forums/showt...with-my-new-BP

What you have done is great, but as far I understand you should use, something to disinfect everything. You can get PAM - Provent-A-Mite which is some sort of a spray based on permethrin again that kills adult mites, eggs and everything in between. Same does the BioKill or NIX solution. Both are also permethrin based.

Hope this helps a bit.