During my first playthrough, I've noticed that the story and some of the quests in Tarant can't be completed as people are missing. For example no one is in the newspaper, or telegraph offices, and also P schuyster (sp?) & sons building.

I have also cleared all the rats in the warehouses, but don't have the option to report this to the halfling/gnome outside.

Well, I guess this serves me right for playing the game unpatched. :P

I played the game unpatched the first time and there was no missing persons it must be something else.

Never had this issue but you really should reinstall and start anew (with all the patches).
No problems for me so far.