Thanks Germania, you were pretty much spot on. Though the cache wasn’t on OneDrive, I did change Temp Directory to an external drive. I thought it would be more efficient to have the temp files on the same drive as the downloads..
Since I changed the temp location immediately after installing both versions of SF, I guess this caused the problem. It should’ve been fine, but maybe the external drive letter changed or the mounting was slow, or it just didn’t like that location. Regardless SF is saving the login info now with the default location and I don’t want to mess with it.
Just note, the files I copied from the my old setup didn't keep any login info, but did copy my SF settings. Also moving to 6.2.0.4 (probably starting 6.2.0.2 and newer with the new CEF) all login info needed to be entered once again, and the new versions prompt the password manager shown in the top post, but it is not needed for SF to keep auto login.
So again thank you for the help, it was key to resolving this problem!