This is a development related question. Please see this thread: http://pkp.sfu.ca/support/forum/viewtopic.php?f=8&t=8796#p53793
Basically it appears that any style changes on the blocks within the Journal are not site-wide. I have chosen for my journal to have leftSiderbar only and styled it with that in mind. The changes do not propagate across the site (one level up from the journal - think of site administration). The suggestion to that thread was that you need to update the database for these changes to become site-wide.
Is there a developer’s guide listing what would need changed in that case?