iframe is being stripped for me also.
Fresh install of Plone 3.3.1
Zope (Zope 2.10.9-final, python 2.4.4, win32), etc.
Windows XP service pack 3
I removed embed and object from the nasty tags.
I removed iframe from the stripped tags.
I added embed and iframe to custom tags.
I think I can eliminate kupu from being involved since I set my editor to "Basic HTML textarea editor"
However - I do have a workaround.
I discovered that the object tag is not stripped (after removing it from nasty tags of course).
So I replaced iframe with object. I had to remove or exchange some of the iframe attributes such as frameborder for border, or src for data. For example:
One caveat, documentation on the object tag says that support varies across browsers - so your mileage may vary.
Jeff