On diffrent occasions i had to clear the squid cache. Squid was not cooperative in reloading newer versions of flash animations or updated pages.
Were you using the appropriate (browser specific) key presses to request that the cache be bypassed? I think it's ctrl-F5 for IE, shift-ctrl R for mozilla/netscape.
If you were using the correct keypresses, then that would mean there is a bug in squid, so you should report it to the bug tracker. We'd need to collect network traces to investigate.
Caches shouldn't need to be cleared - they should work correctly.