Just installed Flash Player 10.3 on Windows 7 64-bit with Internet Explorer 9 (9.0.8112.16421). SWF displays in upper left corner of screen instead of the proper location. First time this has happened with Flash Player. Looks like Adobe has a major issue with this release!
Found solution!
Steps:
1. In IE9 menu select Tools … Internet Options … Advanced.
2. Check "Use software rendering instead of GPU rendering".
3. Close all instances of Internet Explorer.
Adobe should address this issue!
5/24/2011: Update – Problem appears to be specific to IE9. Adobe is addressing this issue and releasing an updated Flash Player version shortly.
3/6/2012: Update – People still searching for this issue. It’s fixed – just update your Flash Player.
By John Dorsey IT Brigade Inc. 
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Flash
Adobe, as3, Flash CS4