We live in an 1890's home with a rock basement and half crawl space half basement. The toilet is situated right between these on the main floor. When we flush the toilet the water comes pouring in through a hole in the wall (it is an interior wall in the basement) The soil pipe to the septic goes out just underneath the main floor (not into the basement floor) We replaced the wax seal and know that is not the problem. Is it possible that the plumbing lines come down into the crawl space and over into the main basement and that's why it is leaking into the basement on an interior wall (it is the wall dividing the main basement and the crawl space)? Please help that corner smells like an outhouse!

It sounds like the stack vent in the wall has holed out and sprung a leak and now you have raw sewage leaking into your basement. You will have to track the leak back to the source. You may have to open up a wall to do this but it must be done. The present setup is not healthy for your family.
Good luck and let me know what you find. Tom