If your squid proxy is not working after rebooting your PC it is possible that this is because the nameservers for your pc were not set before squid loaded. This leaves squid with no way to resolve the domains you are trying to access. For me, this behavior occured on a squid proxy I have installed in Ubuntu.
A temporary fix:
Execute in terminal
sudo /etc/init.d/squid restart
A permanent fix:
Edit squid.conf (probably at /etc/squid/squid.conf and specify the DNS servers for your connection by adding the following line)
Note: 10.5.0.1 is the IP of my DNS server it will most likely be different for your installation