I agree with your programming comment and EPGY can be frustrating. My DD8 started EPGY math at Grade 3.5. Because I started her in the middle of a year, she missed some of the basic requirements and had to go through EPGY for clarification on certain problems. You can actually submit your concerns, but make sure you note the problem number in your correspondence. They will actually address issues if they are aware of them.
My DD had the biggest issue with geometry, in that the instructions were not very clear. She finally figured out what they were looking for, but EPGY actually had to e-mail her step by step instructions to get her through. This comes around the 3.5 grade level, so don't be surprised if your DS runs into additional complications.
EPGY is a learning tool for gifted children, so don't be surprised by some of the curve balls.

The good news is that you can hit the lecture button and search for the appropriate lecture to get through the problems.
Good luck!