We've raised these Flash issues directly with our contacts at Adobe, but they're "slippery shouldering" a little by passing the issue off to the browser vendors.
We've specifically added config now to allow disabling of the Flash uploader in Share for these situations. Until Adobe take these issues a little more seriously, it's likely to be an issue moving forward.
On a more positive note, we're hoping in the future that the multiple file upload features of HTML5 will mature (a lot) to match those of the Flash plug-in, so we'll eventually be able to use that and only fallback to Flash for MSIE browsers where it works correctly anyway.
Thanks,
Mike