I'm not having these particular issues except for the timing one, but I'm definitely not a fan of the HTML5 player (yet). I'd also like to use it but it's just nowhere near as good.
Videos open and pause at 0, and no matter what I do I can't get them to play unless I reload until I get the flash player. Seeking is pretty wonky. As well a couple of weeks ago it used a different sound output than flash (Flash would use what my music did, the headset, but the HTML5 player would try to use my speakers, which were off. Seems to have improved now).
Just hoping it improves significantly in the future.