If you try to run notepad again, do you get the same results?
You can change the FreeType library being used by a given bottle by editing its registry. Normally, you'd use "regedit" to do that, but since you're having trouble getting basic stuff to run, you can directly edit the registry file. The file to edit for a given bottle is:
(your home folder)/Library/Application Support/CrossOver/Bottles/(bottle name)/user.reg
You need to be sure you're editing it as plain text, not styled or rich text. If you're using TextEdit, you can change the mode using the Format > Make Plain Text.
Within the file, search for the string "freetype". You should find a line like: [Software\\Wine\\Fonts] <a number>
and, below that: "FreeTypeLib"="libfreetype.dylib"
You can change "libfreetype.dylib" to "/usr/X11/lib/libfreetype.dylib" and save the file.
See if that gets stuff running any better. If we don't solve the underlying problem, though, you'll have to do this for every bottle you create.