As other posters have stated, you only need two pairs (4 cores) for a 100Mb/s link.
I have been running CAT6a since June 2009 and have
never managed to have a short in a cable. I have even mistakenly drilled through one of the cables (In one side and out the other), and haven't managed to damage the cores or short them out. It still works at Gigabit speeds with no problems.
I would check the terminations on each end of the 'faulty' cable and re-terminate them just to make sure it wasn't a faulty connection.
Also have a look at the RJ-45 plug you are testing with and
ensure the gold contacts are completely straight and not bent. Also make sure they are all at the same height when looking at it from the front.
My old RJ-45 crimp tool for some reason suddenly stopped pushing all 8 pins down correctly and only partially pushed down a few and pushed them sideways. Check whether your crimp tool may not be working properly

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For future reference, it's always recommended to test the cable immediately after installation

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Downstream Upstream
Connection Speed: 24276 kbps 1211 kbps
Line Attenuation: 16.5 db 6.4 db
Noise Margin: 1.1 db 6.2 db