Ok, follow up : it seems that after a complete factory reset and reinstall of everything Koreader works well now (so far). I'm on the 11/2014 stable. Am I correct in assuming that this version has the Evernote bug where the login credentials aren't accepted? One change: this time I copied Koreader into the .kobo directory and not into .adds as KSM suggested (in order to retain the installation after a system update)... Maybe this could have caused problems too...
On another note: highlighting in reflow mode doesn't seem to be 100% reliable and highlights bigger parts of the text than originally selected. This is not caused by unsteady hand as it always selects the same larger area of text in these cases. The mapping to the unreflowed document is fine though...
So far I'm happy and reading, thanks for this great piece of software. Hoping for the next stable to iron out these bugs
Edit: and Nickel froze again, likely this has something to do with saving the file, or with KSM not running properly (memory leak or the like), I have no idea... What's especially annoying about this is that most of my Nickel settings are reset... I think I might return the H2O after all, this whole affair really seems to to improve productivity in the slightest...