I upgraded from 3.6 to 3.7 with no issues. After following the upgrade instructions to upgrade to 3.8, i was unable to login to the store, I disabled captcha and was able to login. I see the administration link at the top of the page, however when I click it to access the admin area I get a 404 "page not found error'.
I have another 3.7 store on the same server and have no issues with accessing the admin area, so I do not think it is related to extensionless file names.