tar xvjf vim-7.3.tar.bz2
cd vim73
./configure;make;sudo make install
rehash
vim ~/.vimrc

It is running the correct vim binary, isn't it? I.e. /usr/local/bin is
in your $PATH before /usr/bin? I think that's where ./configure will put
it without --prefix being given.

Also...and sorry if this ground has been covered...

- Are you using a colour scheme?

- Does
  :verbose hi
  give any insight? I.e. are the colours being set by different files in
  the different Vim versions?

- Does Vim give the same result for
  :set term?
  in each case?

- What about
  :set t_Co?
  ?

- Are your $PATH, $LIBPATH, $TERMINFO, etc. the same in both cases; I
  had some problems a while ago where different path settings of some
  kind caused Vim to attempt to use different terminfo libraries as root
  and as a regular user, and that caused a number of headaches.

I hate it when these sorts of things go wrong. It should be simple, but
it isn't! Grrr!

Ben.



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