Code mix between D5 and D6 in Drupal.org CVS

I have successfully maintenance a D5 module then I want to maintenance both D5 and D6 version.
My D5 version located here : c:\wamp\drupal-5\sites\all\modules\counter
and D6 version located here: c:\wamp\drupal-6\sites\all\modules\counter
I try to create new branch "DRUPAL-6--1" for counter module (http://drupal.org/project/counter) but error, Tortoise CVS say need to do "update". I click on "update" then edit the updated file to meet Drupal 6 then click "commit" then make new branch "DRUPAL-6--1" and new tag "DRUPAL-6--1-0" and successful.

BUT ... when I edit my D5 version in c:\wamp\drupal-5\sites\all\modules\counter and create new tag then error again, Tortoise CVS says need do "update", so I click "update" and .... now my counter.module consists of D5 and D6 codes!

Any advise to maintenance both D5 and D6 module?