Playing the basoon does put the hands in unusual positions & it will take time to get used to this. Also you can strain other parts of the body with bad habits causing pain in back, shoulders & neck which can take a long time to cure. Don't overdo things initially & get advice from your bassoon teacher or an experienced player before you adopt bad habits.
Are you using a neck strap or a seat strap? A neck strap puts perhaps a bit more weight on your left hand so you might think about a seat strap if you're using this method. If you're using a seat strap make sure you place the strap well forward on the chair seat, not towards the back of the seat. This tilts the bassoon more upright so that the weight goes more onto the strap than onto your hands. I have also seen a method whereby the musician uses both seat strap and a neck strap, placing the neck strap in the top boot hook and attaching it to the chair arm or back. This takes ALL the weight and some getting used to, but proponents of this method love it.
Not to open an old thread, but I think it is valuable information. My professor, whom is a fox employee over the summers has his students with larger hands fix a piece of maybe 1/4 inch leather to the bassoon with rubber cement where the left hand hits. I've found it to be great and am considering adding yet another strip as my hands are rather large. It really helps form a nice hand, and increased comfort which was still a problem for me many years past when I started.