help with CvS 2 and SF3 3rd Strike

[cybermonkey]

i just tried pal patcher v.1.0 with my image of sf3. and this version can actually open it normally. so i searched the image for protections and pal patcher found the 50 hz protection thing which i then patched. then i burned the image and it works fine so far, only that it is identical to my unpatched and burned image.
so, basically this just confuses me.