During the week I heat using forced hot water using a 1 year old Buderus G115 boiler. During the weekend, I use a wood stove that is inserted in my living room fireplace. The problem is when the oil burner comes on during the weekend for hot water or late night when the wood stove cools, smoke form the boiler backs up in the cellar for the first few minutes. My only guess is the flew for the oil burner is cold, as it hasn't been used during the day, so until it warms smoke will not go up. Both flews are stainless lined and capped. Am I on the right track, and if so, what can I do about it?

You have one nasty problem on your hands.
Before I start let me say that the boiler you have is a extremely good unit.

Some questions and ideas for you.

Is the chimney on a outside wall or a inside area of the home?
Has this problem been there since the original install?
Has the unit been setup and tuned by a professional? (this is important the G115's are not ready to run correctly right out of the box.)
If tuned did the professional service person leave the required chart or information/over fire/underfire/oil pump pressure/draft gauge setting/barometric damper setting/flue or stack temperature/damper door adjustment on burner/and a overall efficiency calculation. (if this was not done STOP messing around and get it done because it may solve your problem).

It will cost you to have the above service performed if the original dealer did not do it. If the original dealer did not do it call them back because it is part of the Buderus install policy from the factory. This is a relative high efficiency boiler at 86 to 88 % and a three pass boiler to boot.They are very sensitive to improper adjustment.

There is direct vent option for this unit and as a last resort you can have that installed. With direct vent your boiler will not use the chimney any more and the unit will vent directly out the side wall of the house.

Link for your dealer for direct venting.

http://www.buderus.net/LinkClick.aspx?fileticket=CeiOCYunujU%3d&tabid=93&mid=633

These are just a few ideas for you. I suggest you contact the your dealer who installed your boiler to get to the bottom of this problem.