The problem you're running into is not some arbitrary limit in Cygwin that you can make go away with a settings change. It's an inherent aspect of the way Cygwin has to work to get the POSIX semantics programs built under it expect.
The POSIX fork() system call has no native equivalent on Windows, so Cygwin is forced to emulate it in a very inefficient way. Shell scripts cause a call to fork() every time they execute an external process, which happens quite a lot since the shell script languages are so impoverished relative to what we'd normally call a programming language. External programs are how shell scripts get anything of consequence done.
There are other inefficiencies in Cygwin, though if you profiled it, you'd probably find that that's the number one speed hit. In most places, the Cygwin layer between a program built using it and the underlying OS is pretty thin. The developers of Cygwin take a lot of pains to keep the layer as thin as possible while still providing correct POSIX semantics. The current uncommon thickness in the fork() call emulation is unavoidable short of Microsoft adding a native fork() type facility to their OS. Their incentives to do that aren't very good.
The solutions posted above as comments aren't bad.
Another possibility is to go through the drush script and see if there are calls to external programs you can replace with shell intrinsics or more efficient constructs. I wouldn't expect a huge speed improvement by doing that, but it has the nice property that you'll speed things up on the Linux side as well. (fork() is efficient on Linux, but starting external programs is still a big speed hit that you may not have to pay as often as you currently do.) For instance:
numlines=`grep somepattern $somefile | wc -l`
if [ $numlines -gt 0 ] ; then ...
would run faster as:
if grep -q somepattern $somefile ; then ...
The first version is arguably clearer, but it requires at least three external program invocations, and with primitive shells, four. (Do you see all of them?) The replacement requires only one external program invocation.
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