Hi Kevin,

Yes, this is a known issue.  It's mentioned it 6.5.0SP1 release notes:
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 If you just installed QNX SDP 6.5.0, be sure to log out and back in again before you install Service Pack 1. If you 
don't, the environment won't be set up properly, and some files might not be installed properly.
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On Ubuntu systems you will have to use "sudo -E ./<650SP1-installer>" to launch the Service Pack 1 installer.

Did you follow these steps to install 650SP1 and still got the corrupt installation?

If you missed any of these steps, you'll need to uninstall 650SP1 using the cleanup utility, then install 6.5.0.
Then log out/ log back in.
Run “sudo –E ./<650SP1-installer>”  to install the service pack.

Let me know if you have any questions,
Natalia