I actually picked up a thermos on the weekend (sounds the same as yours) so that i can take my coffee in the car with me and drink it on the way to work in the mornings.
At 20 cents a cup disposible isnt really an option in my opinion.
I have a cleaner called Vanilla something or other which is designed to be food safe for cleaning your fridge, and it gets rid of odours really well. We even use it in our bin. Could try that on the rubber seal. Ill let you know the full name of the product tonight. You get it at coles/woolies.