If you're using Class or ID styles, make sure your style names start with a letter.  This is a requirement of the CSS specs, but IE will let you break the rule.

I'm not sure if that's the problem that you're having, but I had that on a project I was working on and was pulling out my hair trying to figure out why.

Martyn:

You are going to have to provide specific details of what is or is not working to get help.

In the meantime, I can tell you from experience that issues with CSS inconsistencies from DNN sites are usually browser quirks and not a specific DNN problem.  I say this not to defend DNN, but to let you know that you could look into other resources and knowledgebases to try to diagnose the problem.

For instance, one problem that drove me crazy for days recently was the opposite of what you found, specifically with the old, and yes still beta and unsupported, Gallery module.  It introduces a lot of new CSS definitions on-line with the page when it renders and I ran into a documented limitation on the number of CSS definitions IE can handle.  Certainly a bug in IE, but all other browsers worked fine.  Long story short, the solution was to change the whole Gallery module and recreate all albums.  This happened of course after I added new albums and made other changes.

Good luck.

Carlos