Annoying blank window in MacVim - how to get rid of it?

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:

/Users/<username>/Library/Preferences/

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:

/private/var/db/BootCaches/<XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX>/app.org.vim.MacVim.playlist

/Users/<username>/Library/Caches/org.vim.MacVim

/Users/<username>/Library/Saved\ Application\ State/org.vim.MacVim.savedState