Hi,
I have the same problem and I'm also using Windows 7 64-bit.
I reported several issues with NIOS 9.1 EDS to Altera, including this missing "Run as" configurations. They couldn't find out the problem (their support guys are still running Windows XP!), so I tried testing NIOS 9.1 EDS in a Vista 64-bit system and those Run as NIOS II Hardware configuration items are there.
So this is a problem with Windows 7, which is unsupported by Altera. :mad:
But even in Vista 64-bit there are problems in NIOS 9.1 EDS: when you try to access project's "NIOS II Application Properties" page (right-click project / Properties / NIOS II Application Properties), the Vista's User Account Control (UAC) detects nios2-app-update-makefile.exe as a program from unknown published and wants user's acceptance to run it. But even if you answer Yes, the NIOS 9.1 EDS fails to show that "NIOS II Application Properties" page (there are some Java errors shown).
The workaround to that is to run NIOS 9.1 EDS with "Run As Administrator" option. Then you can access the "NIOS II Application Properties" page correctly.
When I reported this problem to Altera, the reply was:
"
Unfortunately, Vista x64 is not supported either on Nios II. Please see the Nios II download page for supported OS'es.
https://www.altera.com/support/software/download/nios2/dnl-nios2.jsp (
https://www.altera.com/support/software/download/nios2/dnl-nios2.jsp)
"
So Altera's point of view, you should stick to Vista 32-bit. Or maybe you should go back to XP 32-bit, because that's what Altera's support guys are using ... :rolleyes:
The Legacy NIOS 9.1 IDE seems to work better in Windows 7 64-bit, but the Quartus 9.1 programmer has a major bug: it can not produce a bootable EPCS flash file.
So my solution is to continue using 9.0 tools, which work quite nicely in Windows 7 64-bit.
The only part from 9.1 I'm currently using is the USB Blaster 64-bit driver, which in 9.1 is finally signed correctly. However, since I started using 9.1 USB Blaser driver, my system crashes (BSOD) within 15 minutes after the system is started from standby mode. I'm not exactly sure if it's the 9.1 USB Blaster driver, but before I installed 9.1 I had used standby mode daily for several months. Then I just had to remember to turn off the Windows 7 driver signature requirement during initial bootup (using F8 key during boot) in order to get the 9.0 USB Blaster driver to work in Windows 7 64-bit ...
Hope this helps.
Jari