When u say you use PPF-O-Matic to do the patch what do you mean! PPf-O-Matic wont write a protection patch that u can apply, you need to download a Patch before hand. I'll presume that you know this.
what other software are you using? you need to create a Bin image file and CDRWin is the best for this although there are a few others that can, most dont.
Cdrwin should identify the disk you are trying to copy as Mode1 "green blob" and any audio tracks with a "red blob", the file name you use dosent matter (<anything>.bin) and read at 4x to get a good image file. From what you said i would also get a new version of CDRWin as it sound like yours is naf.
Download the correct patch and then unzip it, use PPF-O-Matic to apply the patch to the BIN file, you should get "patch applied successfully", burn the image back to cd at 2x for data and audio.
thats it Easy peasy really.
let us know how you get on.