Snake: after re-reading your post and my answer I just noticed that you said that covers were missing on both your PC and Aldiko ; did you try the latest (2.0.2) release ?
I realized that you were the one who first reported that thumbnails were not working on Aldiko.
I have corrected an error in the XML element name used for covers in OPDS catalogs, and since Aldiko is the only program using these (Stanza uses its own personal elements) I had no way to test it. So I need you