Chase reports and asks:
Also, the folder ~/Library/Mail only has two folders
Mail Lost+Found
V2
All of my mailboxes are contained within V2... is that normal?
Those folders should exist, but at least based on the contents of my own ~/Library/Mail
folder, it's incomplete. I also have individual folders for each of my email accounts and those folders contain mbox files which I assume are the local copies of the IMAP mailstore.

By way of troubleshooting, it might be interesting to know what the file permissions are for the Mail directory.
Open the terminal, and type (or cut and paste) the following command:
ls -l ~/Library/Mail
The results (edited here to show only the relevant line) for my own functional Mail folder are:
drwx------ 13 jaberg staff 442 Oct 13 00:25 Mail
The permissions basically tell us that this a directory and that the owner, jaberg (me) is able to read, write and execute. (The execute permission of a directory is sometimes thought of as the search permission. You need the x in order to be allowed access to the information about the contents of the directory.)
You can also view permissions from Finder by selecting the folder and performing Get Info… from the file menu (or ⌘+i), but you won't get as much information.

You'll find more information about accessing and interpreting file permissions in the Apple Knowledgebase: Troubleshooting permissions issues in Mac OS X
If you're permissions differ from those shown here, you can try to Repair Permissions using Disk Utility (this doesn't require a restart or booting from a different volume) or, if you're comfortable, change the permissions of the Mail folder to match those shown using the chmod
command. You can learn about chmod from its man(ual) pages, accessed from the terminal by typing:
man chmod
Best Answer
Seeing how you have tried to delete all the normal preference files relating to vim settings, ~/.vimrc, ~/.vim there is one more thing to try and that is the Mac Os App specific preference files for MacVim. One good candidate is the MacVim plist file named
org.vim.MacVim.plist
. A corrupted version of that file may be causing the random window to appear.First thing quit MacVim.
Then delete the MacVim related plist files.
You can use the terminal and the following command to help find the MacVim preferences related files.
find / -name ".vim."
The
org.vim.MacVim.plist
file should be located at:You might also want to delete:
org.vim.MacVim.LSSharedFileList.plist
If the extra 'dead' window problem still exists when you reopen MacVim, then try deleting additionally some more files, this time some Cache and Lion Saved State Related files, along with other related files. Again Quit MacVim before deletion of any of the files, to prevent re-saving of the corrupted state of the program.
I observed the following other MacVim related files in the
find
search results, that you can try deletlting to attempt to resolve the issue: