CKAN not istalling selected mods

[Perotis]

It's been a while since I've played KSP, so most of my addons were out of date.  I had some that were installed/updated with CKAN and a bunch that were not.  So, I decided to just empty out (backed up first) my GameData folder and just reinstall everything through CKAN.  However, not all the selected mods are being installed. [x]Science, B9, are a couple examples of ones that are selected but don't get installed.

[DrLicor]

I never had this issue, but maybe it's the following.

When CKAN installs mods, it has it own cache etc. And if you do a backup and reinstall of you game date, in my opinion its wise to just backup you saves, delete the whole KSP folder, reinstall-install KSP and begin with a clean CKAN. Maybe CKAN just messes up with the logs/cache. (don't know this for sure) 

However, in your case, when I didn't play ksp for a long time and mods are not up-to-date anymore, I just update them via CKAN, and for the ones I did install manually, I have my KSP AVS-AddOn checker. So I can update my mods quickly.