I just got this game and I cant even take off. I have included a photograph to show how in windows the calibration utility is almost perfect. But in game you can see that the rudder is too far off to the left, and the actual stick X + Y axis is way in the lower right corner!

Ive tried messing with the sliders that go from 0 - 100 but the calibration is so far off they dont seem to help enough.

Please help

Done a Google and looks like you are not alone. Visit the Saitek forums. Some suggested using the Saitek Profiler too.

I've had my X45 for about 3 years now and it's always been very good for me.
I realised that I didn't know what my "Input" window looks like, so I checked and basically it doesn't move the green or red ( I don't seem to have a red square ) square at all. ( and the green square sits plumb on the left up against the edge of the box. )

It does, however, operate perfectly in game. I do use the Saitek Profile software and have the inputs set in the HOTAS section of the Controls.

All I can therefore suggest is to set the stick inputs in the HOTAS section of Controls and see if it behaves. Also try the Profiler software - I have found it a great tool.
If that does nothing to improve matters, then NineLives' advice is all that is left. I've also found that Saitek have responded to emails/support tickets I've sent to their helpdesk within about 4 days, so you should be able to get some help from them.
Best of luck.

I sent off a ticket to them... after scouring the forums there i still havent found a solution though

I would try the following.
Go through add remove hardware in control panel, uninstall the x-45 first.
Get the saitek utility called nukeusb. Run it to clean up the remnants.
Reinstall it (carefully following the steps (especially the part that tell you to hold off on actually plugging the thing in.)

Should resolve it. At least in my experience this solved innumerable issues with Saitek stuff. I still have 2 x-45's and am the happy owner of an X-52. Great sticks for the cash.

Try IL2 Joycontrol utility. Much better if you have a hotas and pedals.

http://mission4today.com/index.php?name=Downloads&get=1021&mirror=1144