Whoa reviving 4 years old thread but didn't find it anywhere else, so it might help someone :matrix:
Flashing problem is not problem at all. According to manual from http://www.saitek.com/manuals/x52_manual.pdf (don't know why but it was not in the box nor on CD) it allows you to switch profiles on the fly without need to Alt+Tab from game.
Here is the excerpt:
To change the profile on the fly
Press the clutch button. The LEDs on your clutch and on the main POV control on your flight stick begin to flash on and off. Pressing buttons does not affect the game in progress when the clutch is engaged.
Note: When supplied, the clutch is set up so that you must keep it depressed for as long as you want it to be engaged. You can change the way the clutch works via the MFD tab of the Saitek X52 Flight Stick properties window. See Changing the way your clutch button works in Maintaining your controller settings for details.
[*]Move the main POV control on your flight stick up (north) or down (south) to scroll through your profiles. As you do this, the profile names are displayed in the bottom row of the centre section of the MFD.
Note: You can use the MFD to access any folder on your computer. To open a folder, push the POV to the right (east). To move up a level, scroll through the files and folders in the current folder until [...] is displayed, and then push the POV to the right (east).
[*]Select the profile you want by moving the main POV control right (east) when the profile’s name is displayed on the MFD. It becomes the current profile and its settings are applied when you resume the game in progress.
Tip: You can clear the current profile by moving the POV left (west). The buttons on your stick and throttle return to their default settings.
[*]Release the clutch. The way you do this depends on your clutch settings. Either stop pressing the clutch button or press and release it.
So it's not bug, it's feature folks ;)
Manual attached for future reference. x52_manual.pdf
