If you'll create a passwordfile with "htpasswd", it uses crypt(), and that saves only first eight characters.
If you'll create a passwordfile with "htpasswd -m" uses md5 that saves whole password.
Note that usually all passwords in the file need to be in the same format for anything to work.
Glancing at the .txt, the MD5 option works both with Squid 3.1 and 3.3.
So, maybe rename the old passwordfile, create a new one and make a user entry...
Code:
% mv sqpasswd old.sqpasswd
% touch sqpasswd
% htpasswd -m sqpasswd username
Code:
% cat sqpasswd
username:$apr1$blAHBLah1234
The $apr1$ part is the MD5-encoding marker.
Then maybe restart squid just in case, and try to authenticate.