I have cleaned with sts for many years. I have only seen one thing in all this time that turns everything brown like you are describing and so far not a single person has mentioned it. Letting the brass set in the dirty water too long after it's done. When this system first got popular there were some guys that thought it might be a good idea to put a timer on the rig, fill it up, turn it on and go to bed. They learned that all that did was cause them to have to run the same batch again when they got up...you have to pour out the dirty water and take the cleaned brass out of the tumbler as soon as it is done with the run. If you don't do it right away the brass will stain and tarnish very quickly.
It's not a big deal either way as previously posted, just empty the dirty water and rinse as best you can and run it again with fresh soap and Lemishine.
2 hours is absolutely, positively NOT too long...in fact, it may not be long enough. I always run mine 4 hours. If yours get clean enough in 2 then okay, mine failed to clean the primer pockets at less than 4 on old range brass. It doesn't hurt the brass to run it longer at all. I have a 308 case that I sized and have miked out before I ran the very first batch and it goes in the tumbler every time. In years it has not changed dimensionally, still mikes the same.
Someone mentioned having non-stainless steel in there as being a problem...I don't think so, I have used mine to clean all kinds of stuff, including steel, copper, brass, aluminum and even plastic...many times all at once, no problems yet.