After playing around the only solution I have found that works in all the browsers at my disposal (IE7, IE8, Firefox, Opera and Safari) is to move the attribute from the <COL> element and add it to every <TD> element in the relevant column.
I have changed my code so that the 'align' and 'valign' attributes will be changed to 'class' instead. This means that:
'align' => 'left|center|right|justify'
and'valign' => 'top|middle|bottom'
will be inserted into the XML file as if it were
'class' => 'left|center|right|justify|top|middle|bottom'
This means that existing screen structure files will produce the desired results without having to be modified manually to change 'align/valign' to 'class'.
I will release these modifications at the end of the month, but in the meantime you can test them out in the online demo application.