I'm using moodle 2.1 now but I have, or had, a 1.9 site which I kept as a sort of storage for material I'd previously created and was slowly copying (manually) from site to site. Today though, I decided to upgrade this site to 2.1 to see what happens. Curiosity, mostly. Also, I'd been looking at various open-learn courses from the OU which come in 1.9 format and which (at least my) moodle 2.1 refuses to import. So, I upgraded. No problems there.
I got the 'wrong format' database message too and after baffling myself by looking at myphp, I used the script method mentioned in the second post, by Tim. Worked perfectly.
For any non-expert like me who doesn't know how to start the script, just add it to the url of your site in your browser (so, wwww.mysite.com/admin/innodb.php) and hit the go button. Takes a minute or two, but that's it. Moodle seems to be all smiles afterwards.