Easy to forget in the excitement of upgrading is this workaround from Todd Kopriva's notes on the After Effects 9.02 update, and remember the end note:
"There's now a preference (in the Preferences text file) to control the interval checking done while rendering QuickTime movies through the render queue. By default, when using the render queue to render a QuickTime movie, After Effects flushes the rendered frames to disk every 10 minutes. This is done to preserve as much of a completed render as possible in case the application crashes unexpectedly. However, incompatibility with certain versions of QuickTime can cause the render to stop at this 10-minute mark. If this occurs, you can change the following new setting in the Adobe After Effects 9.0 Prefs (Mac OS) or Adobe After Effects 9.0 Prefs.txt (Windows) file to 0 to turn off this check:
"Flush RQ Rendering Every X Seconds (0 = off)" = "0"
Note: Turning off this check (by setting to 0) will no longer preserve a portion of the completed render, but can allow the render to complete without stopping. Also, this setting will not appear in the preferences file until you render with this version of After Effects 9.0.2, but you can add it manually before launching After Effects."