I tried a little bit to understand these problems...
1) I can't replicate the update error. I even tried the auto update feature and everything worked fine!
2) as regards the cover view, this is the situation with png files: they are correctly displayed in the cover view page as thumbnails. The problem occurs when tapping on a png cover: you'll get a question mark instead of the zoommed image. This is my fault as I use the 0.jpg image (better quality than the thumbnail) but I didn't think about png!
I will easily solve this tomorrow!!
If you still can't see any png image even displayed as thumbnail, this could be related to a bad png file. I use imagemagick (provided with the kindle itself) to create thumbnails: it is really "choosy" with image extensions. It won't work if you just rename a jpg to png. Anyway, I didn't ever have any problem with real png both from comics and from google!
To check if this is your case, you can easily browse to your comic folder and look for two images named "previewlandscape.jpg" and "previewportrait.jpg"!
If you can't find them (even if the cover view is ON and you restarted Komic), then the problems are the images themselves!
3) finally, I created a new folder made of some png and then a mix of png and jpg (everything choosed randomly from google). I changed both contrast and brightness and then played around with next/previous/jump.
I didn't get any problem: settings are applied as soon as the image loads!
The scroll box is in the right place (on the bottom of the screen regardless to where you are in the page!).
Note that I tried everything above both in portrait and in landscape mode!