New theory:
Even though I think I've fixed this bug, I have been experiencing other frustrating issues:
For me I think a lot of my issues I've been having with Finder window sidebar items missing, open/save dialogs missing sidebar items, Recent Items missing, Open Recent missing, etc, etc, etc, have all been due to some corrupted files that got copied over when I used Migration Assistant after the El Capitan upgrade. The reason I feel this is the cause is that the other day I tried to open a label creation/printing app and it wouldn't open. It had been opening slow for a while but this time it just hung. So I created a test account on my system and when I tried to open the app there it opened just fine. Also I could use all of the broken things mentioned above without issue. Granted I was only in that account for a short while but it sure looks like my troubles are contained in my user account and not system wide. So I'm going to wipe the drive and restore files and folders manually. I'm not going to let Migration Assistant copy over all of the preferences and settings and everything. It will take some time not only to rebuild everything but to go through and set it all up like I like it. But for me I think it is the only way to clear up some (hopefully all) of these issues. Just wanted to throw that out there.