Thanks for all the feedback guys.
I've finally found something that gets Whispersync working for me. I have no idea why it works after this but it just does.
I keep all my Calibre eBooks in two formats: EPUB and MOBI. All I did was:
1- delete
all EPUB files, I was then left with MOBI files only;
2- convert those MOBI files to EPUB;
3- delete all MOBI files, I was then left with EPUB files only;
4- convert those EPUB files to MOBI.
Unorthodox, cumbersome, ...but I got it working. I've tested with 7 MOBI ebooks that where giving me problems before and presto, Whispersync is working just fine. Just converting EPUB>MOBI or reconverting MOBI>MOBI didn't fix it for me, I had to go MOBI>EPUB>MOBI as described to get it working.
Thanks again for all the feedback.
