I just tried to profile Clootils.exe (the sample that comes with the Cloo distro) with CodeXL, and after some trial and error, I was able to get CodeXL to work.
I had to first rebuild both Cloo.dll and ClooUtils.exe with the Platform target set to x86. Using the default setting of "Any CPU" gave me a "The application was unable to start correctly (0xc000007b)." error. Trying "x64" gave me a "Failed to profile" error message, and left the ClooUtils.exe process in memory. But trying with "x86" allowed me to profile just fine. I tried both "GPU: Application Trace" and "GPU: Performance Counters" profile modes in CodeXL, and both worked.
So that may provide a workaround to allow using CodeXL.