table prefix - update not working

Not a bug. Documented limitation. Not to be rude, but did you RTM? From README.txt in Domain Prefix.

4. Drupal Upgrades

Running Drupal's upgrade script [update.php] respects the table prefixing provided
by Domain Prefix.  That is, if you run the script from one.example.com, it will update
tables prefixed for that domain.

However, without hacking the update script, we cannot force ths script to update tables
for all domains.  In order to update you site correctly you must follow these steps.

  - Go to update.php on your root domain [example.com].
  - Click 'run the database upgrade script'
  - Expand the 'Select versions' fieldset.
  - Make a record of each update to be performed. That is:
      - If a module indicates "no updates available", ingore it.
      - If a module indicates a number, write down the module name and the number.
  - Run the update script.
  - Check for errors.

Then you must follow these instructions for _each_ domain that uses table prefixing.

  - Go to update.php on that domain [one.example.com]
  - Click 'run the database upgrade script'
  - Expand the 'Select versions' fieldset.
  - Select the appropriate updates that you wrote down.
  - Run the update script.
  - Check for errors.

There does not appear to be an automated way of doing this process.