@unboggling - the Modify ePub plugin uses *exactly* the same settings that a calibre conversion does. So a change to the default page settings would work for both Modify ePub and a calibre conversion.
@Themus - thx for the email, I will hopefully take a look at it tomorrow. If you can do me a favour and send me the other two epubs as well (the orginal and the one that you have applied Modify ePub to that you say does not work on Aldiko). The less work I have to do hunting things down or guessing what you might have done, the more likely I can find time to take a look