Hi Carlo,
A couple of things.
1. Every file and folder in the system is not included in the registry. It does have a great many, but nowhere near all of them. So removing everything relating to "Mafia" from the registry will not necessarily remove all files and folders from the system.
2. There may be entries in the registry that relate to "Mafia" but do not contain the word "Mafia" anywhere in them - they may be in coded form and extremely difficult to find. Frankly, I'm surprised you found any after running Revo in Advanced Mode as it generally finds and provides the option to remove all such related items - but we're dealing with a special case here.
3. IMHO, the problem is that the program was either corrupt (possible, but not my first choice) or was intentionally or unintentionally modified (revising some files, adding files, removing files) and essentially changing it from the official version (possibly or probably to bypass security protecting the software from exactly what was done or even to maliciously alter things to include malware, ways to access the computer with special hacking programs, or create problems such as you are experiencing - again, possibly intentionally, but in this case most likely a side-effect of some other alteration). Since we don't know what was changed (they could have altered actual system files and then disguised it well enough so it isn't being detected), it's almost impossible to identify the cause and resolve the problem (short of something drastic like a clean install or a restore to factory settings and starting over again - I'm not sure if a system repair/upgrade will help, but if you have a genuine Vista installation disk, it's probably worth a try before the much more drastic clean install) as we have seen with the many different approaches attempted already - many of which should almost certainly have worked (and probably would have worked with a legitimate program from legitimate sources).
4. Ubuntu is a good suggestion because it uses a different Operation System and, as such, may work when using the system's OS (even if done from DOS on a boot disk) isn't doing the trick. It's certainly worth a try. The worst that will happen is it too doesn't work (and you have a good disk to keep as it may come in handy for other purposes). And who knows, maybe it might even work (in which case many of us will be thinking that option a whole lot earlier than we did in this thread if we ever encounter something like this again).
After this, and short of something a bit more drastic than warranted (I mean, after all, it's only two or three unwanted and worthless folders that aren't causing any harm where they are - assuming you really are completely clear of malware or intrusions or other problems which have yet to be revealed), I believe most of us will have exhausted all our ideas (though I could be wrong - but I know I have no further suggestions that aren't overly drastic).
I sincerely hope Ubuntu does the trick. Assuming nobody has any better ideas or anything else that hasn't already been tried, how far you want to take it after that if it too doesn't work is entirely your decision. If you have all the software and drivers and codes and backup your data and make note of your settings and put forth the time and effort to essentially re-install and re-configure everything, then I'm almost 100% certain a clean install (or a restore to factory conditions) will solve the problem. Frankly, I would just live with the problem before I went to that extreme, but it's your computer and your choice to make. If you decide to go that route anyway, then post back and we'll provide assistance with instructions or whatever help you need.
Good luck and best wishes!