I resolved the issue, leaving my experience here just in case someone else finds this useful -since SL+MEF is a pretty common combination.
Not sure why -posting on SL now- but when debugging OOB the
was pointing to somethig like this:
Hence it was not resolving the relative paths properly.
When I checked the properties on the web app (right click in the project > properties > Silverlight Applications) these was the order of the SL apps there:
So, removing them and adding them back in this order:
Fixed the issue and now the relative Uri for the xaps I need to download with the DeploymentCatalog is being resolved taking the MainApp.xap as the referece -as it should be.