Sounds like something went wrong during the installation.
What operative system (which Windows version) are you running it on?
I'm just curious to know because of the iCloud conflict, I have it also and didn't get any conflicts while testing.
Could you please check if the following folder is on your machine: C:\Program Files\Bongo 2.0 (64-bit)?
If it is there, is it empty or are there any files in the folder?
The easiest fix is most likely to go to Control Panel > Programs > Programs and Features and uninstall Bongo and then download and install it again while having iCloud turned off.