As a few people have pointed out on the R11 release comments page, I broke the HUD in Mario 64 in R11 :(
I investigated a little, and it turns out it was due to a tiny change I made sometime on Saturday. Basically I changed the alpha threshold test from >= to >, and so nothing with an alpha of 0 is ever rendered. This shouldn't be an issue, except for the bizarre render states that Mario sets up to render its HUD.
I don't think this is a too significant issue as Mario is just as playable in R10. I'd rather release R12 a little early to fix this than mess around releasing an R11b version or whatnot. We'll see how things go with the SSB work.