There's really no difference in how the profile is created. The wizard just seems to be a way to do this all at once, rather than one at a time. Do you have any changes to your gain and response settings?
If you had the calibration window open as you played XWA in mapped mode, would you be able to tell me what value you have on x or y before it starts registering movement?
Dunno, I tried the wizard once but it has a 32 buttons limit that disables some of the buttons on the throttle, it's possible it does other things too but since that was a turnoff anyway I never delved further on what it does and did my profiles from scratch ever since.
It's not that complicated really, you only need to keep in mind that older games accepted a maximum of four axes: X,Y (stick), z (throttle) and r (rudder), just assign the desired value to the axes you need to use and then put them under "control manager device 1", the buttons you can map directly in the software apart from the first two or three for main functions like the fire buttons or the afterburner since many older games don't tolerate too many keyboard command at once (like for example cicling targets while hitting the afterburner), in Freespace and X-wing Alliance I assigned the rudder to the ministick x axis this way by tranforming it in the "ch control device 1" R axis and disabling the throttle wheel.
I'll see what I can do (I am at work most of the time lately), but from what I remember X-wing alliance doesn't like alt-tabbing that much on my rig.