Root Gone but still works for many Apps
Having "root" just means you have a working su binary installed (the "su" application is generally just a management front-end for the linux-level binary installed in /system/bin or /system/xbin).  So, something has gone wrong with the binary, or the way its installed, or its permissions, or its location, or ...

I suspect the apps that still work must have chown'd themselves once at setup time?  So they only need su to work once, and after that they're good to go.

If you can connect an adb shell or run an Android Terminal (that was just the first play store search hit, I'm not endorsing that specific terminal), type "su" and see if you get a meaningful error.  You can use adb to copy a new su binary over, or just re-"root" the device.  See the FAQ questions here: http://androidsu.com/superuser/faq/