The iBookstore books are only designed to work on apples devices. That's why the ereader cannot read them properly.... welcome to the wonderful world of DRM. I can't really blame apple as it's the publishers that make Apple do it. From what I've read the DRM is pretty strong, but that was a little while ago, things my have changed.
I've had calibre for a little while now and what I've learned is every time i open it (or read about it in this forum) I learn something new. It truly is an amazing robust piece of software. I'm truly surprised the programer (member of this forum) has not been written a fat cheque buy one of the ereader companies yet. I like to think of it as photoshop CS for ereaders. 90% of photoshop CS users only use 10% of the program, I feel the same way. It has everything for everyone even though you my not use it to it's full potential the option/feature is there when you need it.
Have you tried to look at the news setting in calibre? Maybe uncheck the ones that you don't want synced.