I understand that there are some problems associated with configuring 
Squid (2.5S6 + patches) as a transparent proxy.  Are there any negative 
affects from having a transparent config even if the browsers are 
directly addressing the cache?

On my (Linux, RedHat v9) LAN the browsers should all be configured to 
point to the Squid proxy.  However there is the occasional lapse, such as 
from newly-installed browser or a guest system on the network.  I would 
like to have a transparent config in place to ensure that all HTTP 
traffic goes through the proxy, but not at the cost of introducing 
problems for all the correctly configured browsers.

So, if I enable transparent proxying with these options:

  httpd_accel_port 80
  httpd_accel_host virtual
  httpd_accel_with_proxy on
  httpd_accel_uses_host_header on

(together with an iptables rule) will there be problems on the browsers 
that are already explicitly configured to address the proxy?

Thanks.

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