[leslamarch]

If I had to guess I would say your missing these ?
make sure you do a back up before trying this, and check your database to see what ones of these are missing.

ALTER TABLE `respawn_times` ADD `instance_id` SMALLINT DEFAULT '0' NOT NULL AFTER `duration`;
ALTER TABLE `respawn_times` DROP PRIMARY KEY, ADD PRIMARY KEY (`id`, `instance_id`);

ALTER TABLE `character_` ADD `instanceid` SMALLINT UNSIGNED DEFAULT '0' NOT NULL AFTER `zoneid`;
ALTER TABLE `character_` DROP `instZflagNum`;
ALTER TABLE `character_` DROP `instZOrgID`;

ALTER TABLE `npc_types` ADD COLUMN `version` smallint(5) unsigned   NOT NULL DEFAULT '0' after `Accuracy`, COMMENT='';

ALTER TABLE `spawn2` ADD `version` SMALLINT UNSIGNED DEFAULT '0' NOT NULL AFTER `zone`;

ALTER TABLE `player_corpses` ADD `instanceid` SMALLINT UNSIGNED DEFAULT '0' NOT NULL AFTER `zoneid`;
ALTER TABLE `player_corpses` ADD INDEX `instanceid` (`instanceid`);

ALTER TABLE `traps` ADD INDEX `zone` (`zone`);
ALTER TABLE `traps` ADD `version` SMALLINT UNSIGNED DEFAULT '0' NOT NULL AFTER `zone`;

ALTER TABLE `ground_spawns` ADD INDEX `zone` (`zoneid`);
ALTER TABLE `ground_spawns` ADD `version` SMALLINT UNSIGNED DEFAULT '0' NOT NULL AFTER `zoneid`;

ALTER TABLE `object` ADD INDEX `zone` (`zoneid`);
ALTER TABLE `object` ADD `version` SMALLINT UNSIGNED DEFAULT '0' NOT NULL AFTER `zoneid`;
ALTER TABLE `object` DROP `linked_list_addr_01`;
ALTER TABLE `object` DROP `linked_list_addr_02`;
ALTER TABLE `object` DROP `unknown88`;
DELETE FROM object WHERE object.type=1 AND object.itemid!=0;

ALTER TABLE `doors` ADD `version` SMALLINT UNSIGNED DEFAULT '0' NOT NULL AFTER `zone`;
ALTER TABLE `doors` ADD `is_ldon_door` TINYINT UNSIGNED DEFAULT '0' NOT NULL AFTER `dest_heading`;

ALTER TABLE `npc_types` ADD `adventure_template_id` INT UNSIGNED DEFAULT '0' NOT NULL AFTER `npc_faction_id`;