We have a whole load of flash animations that use to handle perfectly in Moodle; now however since resources are being displayed through view.php and not file.php none of these files display correctly anymore!
These flash animation files consist of two swf files, one that is the place-holder and controls of the animation and another that is the actual content. The place-holder flash links to the content and displays it within the controls.
Since upgrading to 1.9 the placeholders will only load now and it will not link to the content. This has made almost the whole of our Years 7, 8 and 9 Science courses unusable.
I have attached one of these animations so you can have a look and see what I mean. It is two files zipped up that need extracting into teh same folder. If you link to the file as a resource (through view.php), it does not play; however if you use the direct link (through file.php) it works fine.