I suspect that minor changes in the configuration of the tailpipe can make a big difference. I never had a problem with exhaust coming in the back window of my 94 4Runner as long as it had the stock exhaust system. Once I had it replaced at Meineke I started having problems - even though the tailpipe Meineke installed was visually similar to the stock one. I had the tailpipe replaced again later, and the problem isn't as bad now. Small differences in exhaust system/tailpipe configuration may explain why some 4Runners have this problem and others don't.