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Thalin DeShaker experiment - why didn't this work?

Using the Thalin DeShaker in VirtualDub I went through the first step - video analysis pass which writes to a log file. When the analysis pass finished instead of then going to step 2 and saving I exited out, then reloaded the file and *then* did the second pass. The "DeShaking" message happened which I would assume means the analysis data is applied to the file but the end result after subsequently saving the file was a mess.

Why wouldn't this work? Why would the log file care if the file got closed and re-opened later if the analysis is based on the exact same file?

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