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You are awesome! I would just have chalked it up to bad software on altera's part. I turned off the fancy graphics options like you siad a nd voila, megawizard works like a charm. I am running ubuntu 10.04/amd64 with quartus 10.0
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I also ran into this exact symptom, but running Quartus II 14.1 under Xubuntu 14.04 which means that Compiz is not a suspect in my situation. Now here's where it gets interesting. I had edited the parameters of an existing ALTPLL megafunction before without any sort of hangs or other problems on the very same machine just a day or two earlier and had not changed anything meaningful about my software environment. This had me very puzzled, so I tried the usual suspects (clean project, google search, even attaching to the offending process with strace (it was in a tight wait loop writing {0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00} successfully to fd 3 (an event interface of some sort)) but nothing stuck out at me aside from this thread.
On a hunch figuring that this would be a library API or environment issue I remembered that the day I had successfully edited the PLL I had happened to start quartus from the command line by going to ~/altera/14.1/quartus and typing ./bin/quartus for no other reason that I happened to be at a shell poking around after having done the normal "mv linux64/libcurl.so.4 linux64/libcurl.so.4.backup" drill to make 14.1 work on Debian derived Linux flavors without dying of a SIGSEGV in libcurl.so.4 every five or so minutes.
I get the sense this isn't so much bad software as just the ever present difficulty of managing the complexity inherent to a large software package standing on the shoulders of many external libraries and system functions which we then want to run on many different base configurations. As a nearly lifelong computer programmer (and a latecomer to electronics / digital logic) I appreciate how difficult this problem is, and how quickly the complexity grows as you add in variables.
The takeaway is that if you are not fairly comfortable troubleshooting application behavior in a Linux/UNIX environment it would definitely be a time saver (and worth some piece of mind) to stick to the distributions that are officially supported (or at least direct derivatives like CentOS) so as to tread only on a more well worn path. If you are a dyed in the wool Linux nerd and feel strongly about your distro, be prepared to need to do a bit of troubleshooting / black box debugging.
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