Yep. Ebook formatting is a problem that baffles me. I just completed a new book and the conversion process with the conversion formatter(s) was tedious, harrowing, and at times...frustrating. It took a few months (and not a few dollars) just to get the conversions to look professional. Although the way my book is formatted did pose some difficulties, why on earth in today's technological world do these limitations exist? I will say that the final ebook formatter I worked with did a great job and was exceedingly patient.
I and my editors spent a LOT of time formatting my manuscript but then had to make concessions in keeping it looking the same way in an e-reader due to the limitations of the conversion processes (MOBI and EPUB). After a considerable amount of code strips and revisions, we got them looking good but sheesh...the horror of it all!
