I've got a bit further with this, I don't think it's a problem with the upgrade after all, I think it's just a problem with the file format of one of my sql files.
Strangely it's creating all the tables in the sql file so those commands are OK but all the insert statements between the table creation seem to be ignored.
Looking back at my old code it looks like I hardcoded the sql into the zencart sql where it worked OK.
Any thoughts on why the insert commands don't work would be appreciated. This is an extract from the file - both the tables are created but no data inserted. The file imports fine both as an sql patch and from the command line.
DROP TABLE IF EXISTS `admin_menu_headers`;
CREATE TABLE `admin_menu_headers` (
`id` int(11) NOT NULL,
`header` varchar(16) NOT NULL default '',
UNIQUE KEY `id` (`id`)
) TYPE=MyISAM;
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (0, 'Third Party Mods');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (1, 'Configuration');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (2, 'Catalog');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (3, 'Modules');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (4, 'Customers');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (5, 'Taxes');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (6, 'Localization');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (7, 'Reports');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (8, 'Tools');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (9, 'GV_Admin');
INSERT INTO `admin_menu_headers` (`id`, `header`) VALUES (10, 'Extras');
DROP TABLE IF EXISTS `admin_visible_headers`;
CREATE TABLE `admin_visible_headers` (
`header_id` int(11) NOT NULL default '0',
`admin_id` int(11) NOT NULL default '0'
) TYPE=MyISAM;
