I had the same problem on our relaunched site (just last month). here is what we did:

just before the last closong tag </div> we placed this little ditty:

<br clear="all" /><!-- without this little
NS6 and IE5PC do not stretch the frame div down to encopass the content DIVs -->

I think that Rhuk came up with this. At leat I recycled it from one of his templates.

It allows the content to push the footer down as far as is needed with the content over running the footer.

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