Hmm.. Sounds weird. Usually if the transparent proxy is configured correctly, it should work no matter what OS is running on the clients, as the gateway routes traffic on port 80 to squid. Are you sure it's really transparent? Have you assigned the correct iptable rules?
Be aware that the local computer hosting squid, will not be affected by iptables the same way clients in the network. I have no in-depth answer to this, other then the iptables is usually configured for you network card (ethX), and the local machine use lo (Loopback) for network traffic in some strange way. (There are probably some gurus here to give a better explanation).