@Themus - I know nothing about Aldiko, but rather more about Modify ePub. PM me a link to a zip containing:
- the original epub
- the same epub after you have run Modify ePub on it that is not displaying correctly
- the same epub after you have converted it with calibre and is displaying correctly
If Modify ePub is not doing something it needs to with covers then I will fix it. It could be Kovid has changed something since I wrote it that I also need to add.
There's a bunch of threads around discussing the impact of doing ePub -> ePub conversions. The effects range from zero to significant, depending on both the book content and what aspects of the book are important to you and whether you look behind the curtains or not. Most times the average user would not notice any difference in the slightest. But if via Modify ePub you don't need to do a conversion many prefer to take that approach and avoid any risk at all.