The skin issue sounds like it may very well be a bug. Due to the nature of the Minecraft protocol, we need to special case the recording player. My own skin only has one layer, so I never would have noticed the outer one missing. I've created a ticket for it. I don't have the spare time to work on the RM atm, so don't expect any quick fixes. This also looks like an issue with recording, so any fixes would probably not affect replays which have been recorded with an older version.
I'm not familiar with shader internals to the point where I would have any clue what could cause such behavior. Try asking on the Optifine issue tracker, sp614x is much more familiar with them and might be able to tell you/us what's wrong and what we need to change in order to fix it.