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It might be smart to keep a virtual box with CentOS or any other supported release just to verify if the problem is dependent upon the distribution or not.
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Not a bad idea at all. My box only has 4G of RAM total (and it is maxed out in terms of what the motherboard will support) so it'd be hard to spin up a VM capable of running Quartus.
That being said, a chroot with a Centos install in it might do the trick so long as the breakage wasn't tied to kernel or kernel module related factors.
The fact that it worked if launched from the command line in one particular working directory, but failed if launched from the desktop icon at first made me think I was losing my marbles until I figured out that it was repeatably tied to that factor.
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