I agree!
I think I already found the solution to one problem, replace the following part (almost at the beginning of the script):
setStyle:function(C,B,D){if(typeof B!="object"){var A={};A[B]=D;B=A}jQuery(C).css(B)}
With this:
setStyle:function(C,B,D){if(D != "NaNpx"){if(typeof B!="object"){var A={};A[B]=D;B=A}jQuery(C).css(B)}}
jQuery throws an exception when you pass "NaNpx" as a CSS value and that's exactly what Shadowbox does.
I also encounter another error: my WMV movies within a shadowbox don't play anymore.
Thanks,
Thomas