Sounds real familiar. Answers that work for your issue are in here.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1251993333<partial quote from this thread>
"ALIGNMENT
You have a bent puppy now -- don't be expecting your rear index marks, etc. to mean what they did when the bike was new. Bending of the frame and swingarm mean that the rear and front tires have a new relationship and you need to learn more about that to relationship fix it and to properly align it.
Trying to rely on reference marks and such with a bent bike is COUNTERPRODUCTIVE -- you waste time chasing marks and things that have done been changed on you by that impact.
You have a crab-cycle now, the front tire and the rear tire may not even be in a single true line any more. More likely you are running two parallel lines with your tires and your frame is slightly tilted to your direction of travel. Don't be amazed at this, some custom bikes are built this way on purpose, especially those with very wide rear tires.
How can you recognize this condition? Your handle bars are slightly turned to one side when running straight down the road.
How do you fix this? Adjust the REAR TIRE using the adjustment bolts.
Your front and rear tires must run at the same angle for the bike to physically go straight. My handle bars are slightly cocked to the right when going straight. This means my rear tire is slightly cocked to the right even thought the witness marks, etc say that it is OK.
Adjust the rear tire as if you were directly adjusting the cocked front tire. Moving the rear tire alignment will move the front tire alignment in a 1:1 relationship. Trust me on this, pavement forces on the tires make this back to front adjustment linkage work."