Sounds like you don't have the AH controls mapped to the correct axes on the devices. At first it's not at all intuitive to set them up.
Open the joystick selection dialog from setup. This is the one that has three lists: AH Control (left), Joystick (center), Joystick Input (right). Select the AH control you want to map, say "Roll Input", then choose the controller you want to use, in this case the Fighterstick. The list of axes and buttons on the selected controller will appear in the right-hand list. Choose the "X axis" and click on "Set Input". Repeat with all other controls. The confusing thing is that all three controls have an X, Y, and Z axis, so it's easy to think you're mapping the throttle to the Pro Throttle Z axis when in fact you mapped it to the Pro Pedals Z axis.
Buttons are a little trickier. They are numbered 1-16 in Windows Game Controllers applet, but numbered 0-15 in Joystick Input list. Again, both the Fighterstick and Pro Throttle both have buttons 0-15. What I did was figure out which button number was associated with each hat switch or trigger button, then mapped the AH controls But 1-But 16 to the Fighterstick and But 17-But 32 to the Pro Throttle, again using the sequence "AH Control" -> "Joystick" -> "Joystick Input" -> "Set Input". Once that is all done, go to the Stick Map dialog and assign game functions to the buttons. Helps to have a diagram of the buttons and hat switches. I'm attaching one I made up. Bear in mind that I use CH Control Manager which installs its own controller drivers, and the hat switch buttons are numbered differently than without Control Manager.