I've never seen any of those issues -- are you sure your Internet provider isn't throttling video packets with DPI or something?
I have zero real proof, but I know for a long time Adobe (Macromedia) was pushing their streaming server and didn't really put a lot of effort into handling streaming/buffering without it and I suspect this just never got fixed as things were "good enough".
If you're talking about streaming .flvs off of a regular Apache setup, then it shouldn't be surprising that scrubbing and seeking are troublesome: static file servers weren't build for that use case.
What would you have preferred Adobe to have done?