I downloaded a program called Briz LUT Converter and used it to convert the .cube to .3dl and that loaded fine in AE - but the Briz converter trial only lets you convert 10 files and then you have to buy it - I don't know if there's any freeware that could do the same thing.
Here are the .mat, .cube and .3dl files from my test, so that you can check them out DrDre:
http://uloz.to/x5Qg2nnT/luts-rar