Taken a look into superuser, I saw that already a few apps had root privileges and were doing fine. Just to be sure I started Titanium Backup and the app obtained root privileges without any problems.
Hm, what could be the problem with CatLog?
Seems that newly added apps can not obtain root privileges...
To be sure my device was still rooted properly (I used OTA Rootkeeper in the past when upgrading to new Android versions) I installed Got Root from the Play market and run it on my device.
One of the tests failed saying:
Failed to obtain root privileges through 'su'.
Ok, not sure why, but somehow my device lost its proper root attribute.
It may have something to do with OTA Rootkeeper but I am not sure. I used it when upgrading from 4.1.2 to 4.2 and to 4.2.1.
Anyway, I rerooted it with the Nexus 7 Toolkit. This is an incredible great piece of software and it works on devices running Android 4.2.1.
No surprise that my Galaxy Nexus phone had the same problems. I used to use OTA Rootkeeper there as well ...