ATX motherboard in M-ATX case = crashes

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My Phanteks Enthoo Pro M was too big for my desk so I put transfered the components into my old microATX - Fractal Design Core 1300 (cheap uncommon case).
Since I had that case though I upgraded the computer from a micro ATX motherboard to an ATX.
To allow it to fit I had to cut a small piece out that for some reason they made protrude.
Then I've just stuck a strip of foam (that's actually dust filter stuff for case modding) so the "ATX" part of the motherboard can rest on it.
The problem is I keep getting crashes, 3 different games and Firefox (I am able to rejoin the game though/just go back to what I was doing, no restart required). Any ideas what it could be?
Also my cables are a mess at the bottom of the case and 2x SSDs in there somewhere too.

SnoYAT6.jpg
 
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Sounds like part of the motherboard is touching the case somewhere. I'd have a good look around. Is the motherboard completely level as tightening the mounting screws when it's not could cause a problem.
 
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I don't want a new case as I've put so much effort into modding this one.

It appears the problem was a faulty PSU motherboard cable; I used the one that came with the PSU (Corsair SF600) which I didn't use when I got it as I had to buy a longer cable pack.

Put the longer one in that's always been in there and no more problems, thanks for all your help though.
 
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