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@IamSam   How does it fare with a blank background? Does it have the white outline? If none, what was the setting you had in Save for Web?

addendum.... This was reported during the time of PS7 and it was suggested in the forum report I mentioned to delete the animation sequence in IR, jump back to PS and re-save a duplicate of the psd file which then should be closed and re-opened to continue work with. IR is now integrated in CS so it should work on the same principle without the jumping around... lol.

 I never tried it as I came up with my fix at the time and have stuck to it since.  But thinking about it now, it's plausible it may work as you've deleted all data of the previous imbedded animation thus it's  like a newly created layer file in pre-animation work state.