You are correct, There are several test builds that didn't check to see if the file contained a DATE + TIME, it assumed that if there was a DATE it was good enough, I believe the public beta on the website has this issue as well as the latest private beta.
I cant imagine a ftp server providing the time but then truncating the minutes to 00, though stranger things have occurred. I suppose for these servers un-selecting the auto detect would be the better solution.
Hopefully I can release 4.0 beta to a few people for testing really soon. Due to all the changes right now the biggest hold up is getting the installer updated and adding support for upgrading from 3.x. I simply don't have the time to do it
I suppose one alternative would be to create a generic installer without any upgrade support. It just might come to that.