Lost some button inputs

[Fender16]

I got a Saitek X52 (Throttle and yoke) and installed the drivers from the CD and I had to re enter all the inputs manually. It sucked but only took 5 minutes.
While doing that, I found that some buttons on the throttle no longer register in the game.
I checked them under game controllers and they were detected when I used them but they just don't register in game.
So I tried installing the drivers from the CD again and all that got me was re entering my stick inputs manually with the same buttons not registering in game.
Any ideas?

[lothmog]

Check if your "clutched" function is turned on for the Throttle (believe it's on the GUI tab in the stick set-up).  You'll want to turn it off if I recall correctly.  If on, the thumb button on the throttle acts as a secondary/combo-button and not a stand alone button.

If you're referring to the loss of the mouse pointer/joystick, you may need to install the Saitek software.  I never have.

[Fender16]

I am not seeing this GUI option.
Could you explain it a bit more?

I should have been a bit more descriptive in my post but I did the plug and play for a few days and every button worked.
I popped in the CD to install the Saitek software and that's when the problems happened.

[lothmog]

I'll take a look at my setup once I get home.

If you go to Start - Control Pannel - Game Controllers - select the X52 stick - Advanced.. there should be a tab in the options which allows you to set the LED light settings (dimmers).  On that page, I believe there's an option to "clutch" a button on the trottle which forces it into a mode switch (ie, puch the button and a second button at the same time to get a different action than the button alone).  I'll try and be more descriptive once I get my screen open in front of me.  I'm working on memory alone here.. and even I don't trust that 

Which buttons are you not getting full use of?

And just to clarify, I've only ever loaded the drivers off the CD provided by Saitek.  I then went online and downloaded the most recent drivers for the X52.  I have not loaded the other software packages from Saitek.

[Fender16]

The "Mode" selector on the stick its self but I can live without that.
The button near the mouse control stick (only way I can describe it), the "i" button just to the right of that, and the slider that is to the left of the hat switch on the throttle.
I am downloading the latest drivers and some 220mb software program.
Will let you know how that goes for me.

[lothmog]

The way I understand the X52 setup, in order to use all of the functions on the throttle, you'll need to load the Saitek software (and let it run in the background while playing AH2).  The software allows you to map the controller outside of AH2.  It also unlocks most of the buttons you've listed. 

I have not programed the "mouse wheel" to the left of the 8-way hat switch, or the button to the left of the mini joystick (or the joystick for that matter).  The only button I found to be of issue is one of the buttons inside of the y-axis scroll, which acts as the "clutch" button when the option is enabled.  It doesn't sound like this is your problem. 

Hopefully you'll be able to map all your buttons once you've loaded the software.  Good luck.  <S>