JITs are great but can be unpredictable, that's probably the cause. As mentioned in the article, JITs vs AOT have upsides and downsides.
Re:PyPy.js: Now faster than CPython
by steveklabnik on Tuesday May 06, 2014 @02:15PM
(#7706172)
Doesn't Chrome specifically _not_ optimize asm.js, as well? Wonder if that has anything to do with it.
As the article says, Chrome's performance shows wide variation, even after JIT warmup. It's ranging from 50K/sec to 320K/sec. Bizarre.