I'll also be adding the ability to insert/edit flash objects later in June.

That will alllow snippetmaster to work a lot better with flash..
But in the meantime, Kelvyn is correct.. the editor will try to convert your code to valid XHTML, even if that means killing your old invalid code. Obviously this isn't good in some situations where you may purposely be using invalid code...
I'm currently working on the ability to tell the editor to "leave things alone!!" so that this problem no longer appears.
I should have it ready with the next release, which will hopefully be witihin a week, although I'm now working from dial-up internet, since my adsl went down, and that is causing fairly lengthy delays for me... arg.