Well, don't be upset!
First of all, all the folders included do not create any problems for the program. So, try to begin from the very beginning.
First, make sure you have the latest Image Comparer version installed. The latest version (v3.6) is available for download here: http://www.bolidesoft.com/software/ic_setup.exe
The easiest way to identify duplicates is to use Comparison Wizard. Start the program and if the Comparison Wizard was not automatically launched, use menu item Tools-Comparison Wizard. There you can add several folders you need to be processed (all subfolders will be processed automatically).
After comparison is done, it is better to switch to Tree-like view for the comparison results, it can be done with the "Compare-View results as-Tree". There you can mark the duplicates you need to delete.
Please, once again read help file - menu item Help-Contents. This may be helpful. If any problems arise, then step-by-step write, how to reproduce them.