All of my modules are IPortable, but sometimes on some sites where they are used, they do not export their contents properly.

Why would it be exporting modules on some sites, but then on others it would behave as if IPortable wasn't set?

In the past I had problems with modules not getting registered as IPortable, but I manually corrected that with this sql:
update desktopmodules set supportedfeatures=1 where businesscontrollerclass='my class supporting iportable'

This worked on most sites but today I see this problem on one of my sites again (and I've verified that IPortable is set on the modules in question).

The module export file does not contain the data for the IPortable interface implementation. It is as if the module exported did not implement the interface. Every one of the modules in my site share the same iportable implementation and it works on most sites.

Figured it out. Our export code was dependent on us following a specific (unspoken) naming convention (the fk column in our settings table to modules needed to be named moduleid). It was also dependent on the order by which modules were first installed on the site (any modules that were first installed after the module which didn't follow the naming convention were not exportable).

For anyone who cares, our fixed sql for getting the exported data is available at https://gist.github.com/712000

It assumes that module settings are located in a table associated by a foreign key to modules.moduleid and that this table doesn't have any keys to other tables nor do any other tables have keys to it. actual IPortable implementation and import sql is left to you