Finder error on startup

When I restart my iMac, the Finder goes crazy. This has been ongoing for about two weeks. I went back and searched for those apps I installed during that time - I didn't install any. Here are the problems I am having:

1. I continually hear a soft beeping noise. It is the same noise that you hear if you press a key on the keyboard and you aren't allowed to type, or you try to type too much in a limited text field. Like beeping sounds overlapping each other.

2. One of the folders on my desktop is always selected (usually the HD icon or the one below it). This wouldn't be a problem except I can't select any other folder or file.

3. I can bring up a Finder window, but I cannot select any application which falls below and out of sight (in any view mode). When I try to scroll down, it instantly snaps the display (column, list, or icon view) back to the top. Even launching apps is all but impossible. It's like the Mac is stuck processing (something) and won't do anything else until it finishes...the hideous repeating startup Finder loop.

Nothing I do seems to fix it. However it does seem to resolve itself if I manage to start up an application. Usually it won't let me start up anything - a lot of furious typing and clicking and it goes away. What stops it, I don't know.

I did have TotalFinder installed, but I uninstalled it and restarted, and the problem came back. Repairing permissions and running the gamut with Onyx didn't help either.

Otherwise everything seems to work normally.

Help!

UPDATE: I did try force quitting the Finder, it did not work.

iMac (mid-2011)
Mac OS X (10.9.1)
2.7 GHz Intel i5
2 TB Seagate HD (only 1 year old)
16 GB RAM 1333 MHz DDR3 (1 stock, 1 is 1 year old)