are you trying to do this on Linux? I checked the code and I saw that the comparison between the first line in the file and what is attended (#CC_ICM_FILE) is a bit harsh (it includes also the 'carriage return' character (which is never a good idea, as it is not the same for Unix and Windows systems).
I changed this (trunk version). Let's hope it's the source of this error (otherwise, don't hesitate to send me your example file).
Ok, so it appears that it was a 'unicode' encoded text file (UTF8 exactly) while CloudCompare doesn't handle such enconding styles. It needs pure 8bit ANSI (such as what the classical Notepad tool generates).
I'll try to figure out if Qt could help CloudCompare be more 'subtle'... meanwhile, don't use any other encoding than "ANSI" in Notepad++ (or any other text editor).