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I use IFRAMES relatively well on some of my sites...
Only thing I suggest is the following:-
Ensure the pages are not tripping up on duplicate filter - if the majority of the difference between pages in your site is the contents of the IFRAME then you will know what I mean by this.
Secondly - I would be careful of how much text you have between the IFRAME tags - I would assume that SE would treat to much text in these tags as spam (not seen any evidence on this though) - however you should be able to have enough text to explain what should be in the IFRAME area and why the browsers do not display the IFRAME - after all that is recommended HTML when using IFRAMES and I dont see SE having a problem with this - I did pose this question regarding content between IFRAME tags a few days ago but did not get much feedback unfortunately :(