This will not be a problem for most people, because very few will use embedded Flash. And those that do are not likely to include a Flash object in the snippet because there is nothing there for the program to edit.
There is a problem with Flash movies within a page in that it has usually been embedded - something that is incompatible with valid XHTML. I don't know how you are embedding Flash, but the following is XHTML compliant.
<object type="application/x-shockwave-flash"
data="c.swf?path=movie.swf"
width="400" height="300">
<param name="movie"
value="c.swf?path=movie.swf" />
</object>
This will work in FF etc and also in IE, but in IE it will not stream unless you include some actionscript in the first frame of the movie. Sorry I can't recall the code for that as I don't use Flash. The full XHTML validation list installed with SnippetMaster does include all these parameters, so it should parse OK using the full XHTML ruleset - as long as the rest of the page is XHTML1.0 and with a correct DTD.
The programmers of tinyMCE, the editor in the core of SnippetMaster, have just released the alpha of a new tinyMCE version which does offer support for Flash. How long that will take to get to stable release, or if Henri would be able to use it in SnippetMaster, I have no idea.
SnippetMaster is very easy to set up and works exceptionally well with valid code - this is why it is poplular. It was never intended to be used as a full page editor, but to enable users/owners of websites to be able to edit and update parts of their pages.