It is possible that the GAPDH gene is influenced by the treatment and in this case you need to test another housekeeping.

What is the sources of your RNA? Were they tissues, cell lines, primary cells? If the RNAs were extracted from tissues or primary cells, they mostly came from mixed different cell types, which could result in different RNA compositions because of different proportion of different cells. Choosing house keeping gene sometimes can be very tricky. There have been many researches done, and the basic consent is that having more house keeping gene is more accurate. However, it might not be feasible in lot situations. I would check the literature for similar house keeping gene(s) for similar sample source and treatment to help my decision and trouble shooting.

I suggest to try more HK gene foe exmple : tubulin, elogation factor, RPB2, etc.. try to test in few samples different HK in each different treatment you test in your experiment and you take in consideration only the gene have the same Ct in the control and in your treatment.