FYI, my reply to this thread was answered by Altera support:
On 5/26/14, 2:51 AM, Altera_Technical_Support-AutoReply wrote:
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> The following "From Altera" note was posted by yyyyyyy:
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> Hello zzzzzz,
>
> Your service request has been received. I will be helping you on this issue.
>
> Ubuntu Linux is not the supported OS for Altera Complete Design Suite version 13.1. We never perform any regression test on unsupported OS like Ubuntu OS. It is not strange that Qsys generation fail in Ubuntu OS.
>
> The same project generates/compiles fine on a Windows Quartus II/QSys 13.1 installation because our Quartus II 13.1 does support on Windows OS.
>
> Check table 1 for more details information about Operating System support on our ACDS 13.1:
>
>
http://www.altera.com/download/os-support/oss-index.html >
> I would recommend you to try on RedHat enterprise linux 5 or RedHat enterprise linux 6 (64-bit).