I have modded a few systems now and so far, the only time I ran into a problem was when flashing the custom kernal didn't work right. (I had left the computer on after dumping the original kernal and my computer reset while I was gone and it never tried to flash the custom kernal.
Have you tried to create a new hakchi2 folder maybe even name it "hakchi2 test" unzip the hakchi2.zip file into that folder. Then add the games you want to add. Click on the synchronize button and follow the prompts to boot the nes, then dump the original kernal (do you get an error at this step saying it doesn't match the checksum?) then let it flash the custom kernal and then upload.
Hope that helps, as I said, was the only time I couldn't make it work...