I think the only way to explain all these problems is to clearly define Superman's "turn-back-time" super power. This power obviously doesn't really turn back time 100% - it only "sort of" turns back time, leaving some of the original events in place, but turning back time on others. Plus, most people still have a subconcious memory of those original events, since many of them kind-of-sort-of took place, which explains why Lois is so confused about who Jason's father is.
Yeah..... I personally don't consider SR as official canon to the Christopher Reeves films (first 2 anyway), I know my opinion doesn't matter to Waner Bros. but I would rather watch Superman 3 and 4 than rewatch Returns.