There are a bunch of different possibilities
(*) temporary files - there was an improvement here in recent cygwin versions which means that if your machine has lots
of memory and your program creates lot of temporary files, then it will now be significantly faster
(*) file name lookup - linux has a path name cache, which makes it quite a bit faster then Linux for heavy use (git is
the poster child here)
(*) file information lookup - some of the "default" Unix APIs will look up a bunch of information which is cheap on
unix, but expensive on Windows. Normally there are alternative API which will only load the minimal set of information,
which will then be cheaper on Windows.
(*) spawning - it is quite possible that Latex is making heavy use of spawning child processes to do various things,
which is unfortunately more expensive on Windows.
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