Are you using the Karmic Dice option?
From what I can gather, it seems that the setting ironically makes rolls worse and will actually increase the odds of rolling nat 1's.
As far as I'm aware, Honour Mode doesn't affect dice rolls, it only locks you out of reloading so you can't save scum to bypass skill checks. So any undue low rolls would be the fault of other factors such as the aforementioned Karmic Dice option.
