Sorry for the delay, and thank you for your replies.
Right off the bat here I want to say THIS WAS NOT A FAULT OF PASSWORDMAKER, this was a fault of my own doing. Here is the explanation anyway though.
I changed a couple of passwords before I really understood how this worked. I didn't take note of the settings, specifically the hash settings, so I could not for the life of me figure out what the password for one of them was. I did get the other two, though.
Here lies the problem, which truly has nothing to do with this valuable piece of software, but more to do with my quick-password-change and quick-try-and-recover stupidity, this one password I could not recover was for one of my gmail accounts. When I could not get it to reproduce it, I clicked on the 'forgot username / password' link in gmail. There, it asks for your username, and nothing else on the screen (other than for your password in another field if you have remembered that but not your username). The next screen says it has sent an updated link to my 'alternate' email address which I can click on to sign back in to gmail. HOWEVER, I must not have entered an alternate email address, as I have received no email from gmail at any of my other accounts!
I thought they would give me a link to answer my secret question or something, but that was not an option. They do refer to the secret question in their FAQ, but I was not given that choice, no matter where I looked.
So, at the end of the day, this was my fault, not Passwordmakers and everyone reading should please take note of this.