Are you seating the clip far enough down in it's little groove? Is it possible that the modification is somehow blocking the clip from seating properly? Have you loaded other SKS from clips?
I probably can't give you a solution, but I'd like to know more about the difficulty you're having. Whenever I have problems loading from strippers, it's usually one of two things. 1) I didn't seat the clip far enough down into the gun, or 2) the clips had been loaded a while and the steel edges bit into the laquer finish on the Russian ammo casings, and had to be shaken a bit to break them loose smoothly.
Load the clip up, hold it in one hand over something to catch the rounds, and use your other hand to push the rounds out of the clip as if it were in the gun. Do they come out freely with the normal amount of resistance?