I've done some more investigation, and it appears several things are at play.

The MKS touch I'm using only sets very coarse timestamps. 
GNU Make on windows uses stat which doesn't have high precision on windows. 

After moving to my homebrewed windows_touch and fixing GNU Make to use
GetSystemTime and FindFirstFile
for timestamps, and changed FILE_TIMESTAMP to be defined as unsigned long
long, it works as expected, and my list test script bar.sh runs for a long
time without failing, aka has not failed yet. 
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