This was a support issue but it's not being addressed and it is critical. The product workflow as listed in the transaction view changes to completed after every cron run.

If I set workflow to "shipped" then run cron, the workflow changes back to "completed".

This has been addressed several times under topics such as "workflow not sticking" but noone was able to make the connection that a cron run was causing the problem.

My solution was to do all the tasks manually however, I have just figured out that my site isn't going to index unless cron runs and now I have a problem.

This is a critical bug.
It was addressed here without comment..
http://drupal.org/node/257539

Thanks