I have been using SWFObject on a page which also uses the JSON.js library from http://www.json.org/ - I believe this will also apply to the Prototype.js library.
There is a problem with this because the JSON library adds properties to the global Object prototype. SWFObject includes some unsafe for/in loops to append parameters and vars to the html. Functions on the object prototype are converted to text and then placed into the embed tag, causing corrupt html.
Just to summarise to everyone reading - you are just need to put in an extra if statement to make sure we are only adding properties which are a string or number type to the object/embed code yes?
I know a few people have been banging their heads with incompatibilities with other libraries. It would be great if the above dealt with the majority of the issues :)
Geoff, can we look at making this mod?
As an related aside, I know flash itself had some similar issues (being prototype based also), and you could do tricky things with an undocumeted function assetpropflags. See more here if anyone is interested: http://www.flashguru.co.uk/assetpropflags/.