Do you have a full backup to restore, which will at least get you back to where you were before the OS upgrade? If so, you may want to consider that so you can get back to work, and a working configuration.
Some have reported installing the full OS a second time cleared up odd problems like this. It can't hurt anything to try installing El Capitan again.
Personally, I won't install one major OS over another. I always create a new partition and install it there. Then add all of my third party software as I have time. That allows at least two major benefits:
1) I can keep working in the previous OS without affecting it. Then switch when I'm ready.
2) Any issues between the new OS and third party software won't throw me since I can simply wait until they're fixed. I still have the previous OS to boot to.