Hi, Sam -
I think it was the term "convert" that made me question the replies, since you're not converting
the pdf file, just placing it inside a zipped file. I'm just 'way too literal sometimes
No, I never had any problems (that I know of), but a few weeks back, I did start "packaging" all the files into one self-extracting zip mainly because you can set it up to extract to a specific directory and start up a specific file.
I think it's easier - especially for people new to ebooks.
Good luck on your ebook, Sam - hope mine helped you a bit!