On a recent project (see http://www.wothke.ch/webixs/ ) I have the effect 
that the Emscripten built version of a music player in *some* songs 
produces "incorrect clicks" that are completely absent if the same original 
C code is built as a win32 or 32-bit Linux executable (e.g. see song "world 
of noise" in the dropdown list). 

I think I already fixed all the unaligned memory access issues that the 
program originally had had (at least there are no respective warnings 
anymore - I am building with -s ASSERTIONS=*1* -s SAFE_HEAP=*1*).  for the 
most part the code seems to work fine..  and I would suspect that it might 
be some kind of special case clamping/overflow issue.. 

The audio-generation logic to a large part is based on (unsigned )int64 
based logic (simulating the functionality originally performed by x86 MMX 
operations (e.g. adding/multiplying packed int16 within int64, 
and-ing/or-ing, etc) and  and floating point (double) calculations. Are 
there any known issues in that area? anything that might help me narrow 
down the  the search area?

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