Hi Brandon,
It sounds like you might need to send your files over to
Articulate Support. They'll give you instructions on how to do that.
Are you using the latest version of Studio '09? Your PowerPoint version should be: 6.1.903.321. If it isn't, download the latest trial version, run it on top of your current version and then activate it with your serial number.
Then I would next check that you are publishing at 30 fps in Articulate -> Presenter Options -> Publish
Some animations, particularly SmartArt animations in PowerPoint 2007, will not publish correctly if you aren't using unique text in each SmartArt text box or if you are leaving them blank so you'll need to check those if you have any.
I sometimes find it much easier to time my animations using the Record Narration or Sync Animations tools and then setting the audio level to zero or removing the audio altogether. The timings should stick provided that you publish to 30 fps.
Regards