I've lost a lot of my accessory windows from some random app install To start: I'm a software dev much more comfortable on Windows than OSX. I've tinkered with things like homebrew (which is where I think I started my issue) and I'm not 100% familiar with what I may have done.

The short of it is that in Preview.app, using Export, there is no window. I know that it's trying to create the window, and I've even on occasion seen the controls associated with the window on the very lowest level of the gui stack, if I minimize everything except Preview.app. But I can't interact with anything in those windows. This applies to other windows in Preview.app.

There are other applications installed as well, such as Microsoft Remote Desktop.app (the red icon, relatively recently released) where the Import and Export windows do not appear.

It may be that I had installed XQuartz, but I removed that (and rebooted) and I'm still having issues. 

How can I go about figuring out what library is probably overwriting these menus, or where to look to see what system information can help me figure out the problem?

Here's an example output from Console when I try to open the Preview.app Export window:

1/15/14 7:18:57.137 PM Preview[13893]: RVS:__54-[NSRemoteSavePanel _runOrderingOperationWithContext:]_block_invoke_0319 : Timeout occured while waiting for the window

And Microsoft Remote Desktop.app Import:
1/15/14 7:20:15.164 PM Microsoft Remote Desktop[5529]: RVS:__54-[NSRemoteSavePanel _runOrderingOperationWithContext:]_block_invoke_0319 : Timeout occured while waiting for the window
So it turns out that these two links sent me on my way. Doing a self post in case other people can find my post by googling.

Unresponsive save dialogs in Preview  

http://lists.apple.com/archives/macos-x-server/2012/Aug/msg00291.html

To fix this: Disable "Documents and Data" under System Preferences > iCloud and you're on your way.

This has to be the most aggravating bug I've found in a while. Ugh.