Do you have the damage received percentage set lower as well? That will effect the negative effects you get.
I will look in the code again when i get a chance.
Tested it with 100% damage set and also lowered. In both cases the negative effects were not applied during the raid. They were displayed at the post raid heal screen and I could enter next raid with bleeds, fractures (but tremor from fractures would not show up, same goes for negative effects from some stims, SJ9 for example) etc.