It’s unlikely that you are using the exact same settings, as both applications don’t have the exact same feature set.
Bottom line us that Squeeze is a better transcoding application than Flix, although the codec implementation is probably exactly the same.
Forget Silverlight, if you can’t get Flash to work well at low-bandwidths then you’ll be even worse off with that Windows technology. (IMHO Silverlight is going nowhere).
There’s no such thing as ‘Flash Turbo’ AFAIK.