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Not used Training Peaks, but sounds like the power calculation was made from the non-zero average, ie discounting the period of time when off the bike as opposed to TrainerRoad that included the zeros.
The only real way to know which figure is correct is to run the test again!
As for starting too conservatory, that's the best way to do the test IMHO.
I just did my first FTP test. It was going well (though during my first five mins I was too conservative) but after 12 mins the carcass of my rear tyre ripped. I had to get off, remove the carcass from the tyre then jumped back on and finished the test. Not ideal!
Just uploaded the file to trainingpeaks and its given me a 20 minue average of 15w higher than trainerroad - is this because it smooths out the spikes? It took me about 45 seconds to get off, remove the carcass and get riding again.