1. Rename .emacs to renamed.el
   
2. Start vanilla emacs
3. Open your renamed.el file
4. Select region of intereset
   
5. Evaluate region with M-x eval-region
6. See if it is still working
7. Go to 4
   

There is something in my .emacs that messes up table alignment in
org. Have been struggling to find it. If I remove my .emacs, table
alignment is fine. I have tried commenting parts of .emacs to identify
the offending lines. But somehow I am missing it.

A copy of my .emacs is at: http://dl.dropbox.com/u/10112644/dotemacs

Will be grateful if somebody could help? Is there a way I can load my
.emacs segment by segment and see when the problem appears?

Vikas