If you are looking for a reason a nickeled case would fail to cycle the auto-disk where brass cases did, I don't think you are going to find one until you run some experiments on your setup. Frankly, I don't think that is the source.
I believe the nickel case being the only one without a powder charge is coincidence (unless, as was suggested, having an odd case distracted you).
If you are concerned, you might consider batch processing. Having, as part of your quality control, a gang inspection of 50 cases all at once in a loading block for uniformity of the powder charge is VERY reassuring, even if it slows down your production rate.
Good luck.
Lost Sheep
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