Hi blackwellj, I use a Saitek X52 Pro and have no problems with it.
Like Fred, I don't use a profile but assign commands to the diverse buttons and axis.
Here's a guide how to set up controls in SS2008, it's pretty much the same in Extremes..
http://80.95.161.114/shipsim/forum/index.php/topic,3472.0.html
ps:you may want to register your game here, so you have access to all the other boards (Technical support, etc