Well, I have no idea what is going on but I'm suspecting a hardware problem. In my last reply I was confident the problem was reproducible but as I continued to try things that proved to not be the case.
I switched to working with Chicken-5.3.0rc2 and the build there failed on creation of modules.db, again it was very reliably reproducible. Thinking this was maybe a race condition between the creation of the modules.db file and the following file copy I added a little code to read the file back and compare it. The problem went away. Unfortunately when I reverted the code the problem did not return. That does not make any sense whatsoever.
Currently I'm able to get to where when I install the sqlite3 egg it fails with:
Error: unterminated list
If I run the install a couple times it results in a working egg.
I'll keep chipping away at this but I don't think I have anything tangible to offer in terms of a problem statement other than ... "Windows sucks".