I have 3 stylesheets, style_ie6.css, style_ie7.css and style.css. Here's what I have:
I've used browserlab, ietester and browsershots and IE6 & 7 are ignoring my conditionals and loading up the main stylesheet.
*edit: don't know why it isn't displaying... here's the live link:http://www.inishrosshouse.com/index.php
Depends on what tags you're putting into the ie6 and ie7 versions. First, I'd recommend moving the style.css first. Then only put tags in the ie6 and ie7 that change a tag to make it work in that browser.
I can only speak for IETester but I this is known behaviour there: When multiple instances of Internet Explorer are installed (or active) on the same system, conditional comments will be resolved against the highest IE version available on the system.
Put the main stylesheet before the conditionals.