Our whole house has a strong sewer smell, we have a septic system and the pot has been pumped within the last 3 months. We find that the flush does not always work. Do we risk any health issues from the gas smells?

Strong concentrations over time are not good for your health. Most of the smell is methane, which by itself is odorless and colorless. You can imagine it is not by itself when it leaks into you home from the sewer. Methane is flammable in strong concentration and it also displaces oxygen that you breathe. You won't fall over dead tomorrow but this issue will not fix itself and eventually something needs to be done, do it now. I think a likely place to start is to rod out the vent stack from the roof. Run enouh 1'2" rod from roof toi basement and about 15' more. If that doesn't fix it just come back and add to this same post.