@acee: Did the HumbleBundle supply a CBR or CBZ version? When I have looked at comics on my Kobo device, I didn't find the epub versions to be particularly good, or add anything to the experience. The devices can handle CBR and CBZ natively. The pages will be sized to fit the screen and allow zooming. If the Manga pages are suitable to view without any zooming on most pages, this might be the better method.
Having said that...
You might also want to consider sending the books as kepubs. These have the advantage that they allow zooming on the images. The KoboTouchExtended driver is the simplest way to achieve this.
For the cover page problems you are now seeing, is this the cover that calibre added during the conversion? If so, it might be coded differently to the other pages. You will need to check that separately.
And for either epub and kepub viewing, you might want to enable full screen mode. To do this, add the following the the "Kobo eReader.conf" file on the device:
Code:
[FeatureSettings]
FullScreenReading=true
If you are using Windows, make sure you use a Unix line-end aware editor when doing this. I recommend Notepad++ for any text editing on Windows.
Once the above lines are added, there is an option in the reading setting to show the header and footer. Unchecking this hides them and lets the page display full screen.