As an eZ Publish developer I know that whenever creating an eZ Publish site the cache can be my best friend in production and worst enemy in development. eZpedia has a great article all about clearing the cache.
My favorite is the manually clearing of the cache. For some reason the clear-cache script sometimes misses some files; so the only way you are going to see your changes is by dumping those files manually.
cd /path/to/ezpublish; rm -vrf var/cache; rm -vrf var/ezwebin_site/cache
rm -vrf is very scary to run (remove all?!?), but so long as you are doing
this to the specified directory you should be safe (but be careful).
EDIT: Its worth noting that you should never clear the cache this way if running distributed eZ Publish installation.