Most of the time when this error occurs, it's because you tried launching the game the 1st time you used PH, and the game didn't start for whatever reason. And then you tried launching S4 again, with the same PH open from the previous attempt, this will cause the hacks not to work
So basically everytime you start S4 you need to re-do the PH stuff.
EX.
I start PH, get the hacks I want, and I start the S4 Patcher, but the Patcher stops at Step 7 and gives me whatever kind of error.
The next time I start S4 I have to start PH all over again and select my hacks in order for them to work ingame.
Hope this helped, if even a little bit.