Hi,
Do you use any caching system such as a caching component or the built in System – Cache plugin? As this seems to happen when caching is enabled, what happens is that someone using IE6 visits and gets the warning message at the time when the cache updates itself and then that page is stored and served up to every other visitor until such time as the cache updates again.
If you follow this link the instructions are there to remove the IE6 warning message code http://www.joomlart.com/forums/topic/warning-remove-ie6-warning-if-you-use-caching/ but unfortunately if you use caching this doesn’t just happen for IE6 users it also happens when a mobile or handheld user visits as I found earlier – to my dismay my site had been serving up cached pages of the handheld or iphone template all day to regular visitors. So you may be better off disabling your cache plugin or component if you use one.
I think the cache setting in global configuration is ok to use.