As someone said earlier, increasing 3 out of the 4 lifts is great. I have never seen increases in all four lifts at once in my own training or anyone else's.
Also, this is only your SECOND cycle. You need to stick with this program for 6 months or even a year before really evaluating progress or lack of it. Your squat could labor in weakness for a couple of months and then shoot up out of nowhere, then the other 3 lifts could stall. Training progress isn't linear, nor is it always predictable.
My advice is to complete this second cycle and see what happens. It's likely that you may have to drop your training max on the squat 10-15KG for your 3rd cycle.
Most importantly, remember that if you do have to drop your TM on the squat, it doesn't necessarily mean you got weaker. It's just where your squat is at the moment. My bench has been total crap for several months. Nothing about the lift feels comfortable, and I am putting up awful numbers with it. But my other lifts are increasing, so I am riding that wave. I suggest you do the same. The squat will come around, even if you have to drop the TM for a while.
Give it time.