That's right, the ./bin/install is were all the tables are created.
This was an area where I needed to back and forth a couple of times. When things go wrong, there are some error messages that give a bit of a clue as to where it goes wrong. e.g. mysql driver is use, access denied/refused, unable to create table, etc.
One area that could stop the tables being created is the right MySQL configuration.
You might want to try setting the MySQL configuration with a post-upgrade & reboot (even though the MySQL documentation here
http://wiki.contribs.org/MySQL does not say we need that), but this is one of the things I ended up doing:
/sbin/e-smith/config setprop mysqld InnoDB enabled
/sbin/e-smith/config setprop mysqld LocalNetworkingOnly no
signal-event post-upgrade; signal-event reboot
I also dropped and recreated the funambol database between attempts of the ./bin/install