I ran into the same problem the other day and couldn't find any clear and obvious answers. Did some more digging and found out the real problem was my goof up. SDK gives you two different types of targets: _X86, and _armel. _X86 is used to build apps for testing and running within the SDK; _armel is used to build apps that will only actually run on the tablet/devices themselves.

So if you're compiling an app to test, my problem was I was in the _armel target, so I got the SBOX_CPUTRANSPARENCY_METHOD error every time I went to run the app within the SDK. So, here's the process:

1. login to scratchbox
2. type sb-menu and hit enter
3. From the menu, go down to "Select - Activate a target"
4. Select either Diablo_X86 of Fremantle_X86 (whichever one you're building for).
5. Hit OK
6. Scratchbox will restart, and now you're in _X86 mode. Rebuild your application; it will now run normally.
7. When you're ready to build for testing on a device, do the same thing but this time select an "_armel" target, rebuild your files/package. You will only be able to run the "_armel" version on the device itself.

Hope that helps! It solved my problem!

Thanks!