Here is the Emscripten change which triggered the problem. It changes the alignment of variables which are allocated at compile time. Previously, they were 64 bit aligned. Afterwards, they are aligned as appropriate for their data type. 8 bit values don't need any alignment, and so they can end up improperly aligned for 16 and 32 bit access. This change is in emscripten-fastcomp, between 1.34.1 and 1.34.2 tags. Variable alignment depends on the build used during the final Emscripten link.
This is not an Emscripten problem, but an issue in DOSBox which started causing problems after that Emscripten change. If you think you may be dealing with an alignment problem, link the program with -s
SAFE_HEAP=1. That will cause misaligned access to report and alignment error and throw an exception. You may also want to use a lower level of optimization or at least
--profiling-funcs, so it is easier to find where the problem is occurring.