I've had the same problem. Found a solution on a german fansite.
Before following these instructions make a backup of your save folder!
"If you get stuck by being unable to complete a quest, delete the latest .que file(s) and see if it resets the quest
The quest save files are in My Documents/My Games/Titan Quest/SaveData/Main/[your character name here]/Levels_World_World01.map/[difficulty level where you're having an issue]. Sort these files by "Date Modified" and delete the last one or two. See if this resets the quest for you. In some cases you may need to delete several files to clear the quest.
Once the quest has been cleared from your quest log, you then need to go back through the quest completion steps in order to trigger the final step and move forward. For example, if you've killed Alastor and gone to the docks, but the ship captain won't speak to you, and you quit out and delete the relevant quest files, you then need to return to Athens, kill Alastor again, talk to Phaedrus, go out to the docks and talk to Feiyan, then talk to the ship captain to move on to Knossos.
If deleting the .que files doesn't help
If you can't move forward, make a backup of your quest files somewhere else, like on your desktop, then delete all the files in the quest folder. This will erase all quest data for your character, but you should still be in the same location and have all of your portals enabled. As with the previous workaround, try to pick up the quest again and do the completion steps to move forward. Once you have moved on, you can copy the .myw files back over from your backup.
General tips
Do not leave an area before completing a quest sequence. For example, talk to Phaedrus before teleporting back to town to sell your loot.
Do not create any character back-ups in the SaveData file. This can confuse the game. If you are doing manual back-ups, just save them to a different folder.
If you can move forward, go ahead. Most of the quests will not get thrown by not having completed a prior quest. If you can play MP, this means you can sometimes teleport past roadblocks (like the gate in Memphis).
Sometimes if characters are pushed out of position, the "hot zone" for activating them does not line up with the character model. Mouse around until the dialogue icon comes up and just click there.
If all else fails...
Just delete all of your quest files. You should be able to move forward, and while you won't have the quest log for previous quests, that shouldn't prevent you from completing the game. The portal data is saved elsewhere, so you can always teleport to the most forward city you've reached and move on from there."