Problems Uploading to JTAG Device #2

Is there some configuration step I'm missing that will make the "Upload" feature work properly when the FPGA is Device# 2 on the JTAG chain?

Background:

I'm working with an Altera Stratix PCI Dev board. I've been successful with creating a NIOSII design in SOPC builder, and I can write programs that run successfully. I've also ported Altera's Flash Programming Utility to this board design, and I can flash programs and/or H/W configurations into the flash from within the NIOSII IDE. So far, so good....

Next step was to get uClinux up and running. I figured out a couple of problems with the build environment, and now it seems to be building vmlinux.bin file successfully. When I right-click on this file, and select "Upload" from the pop-up menu, the Upload process fails however. It appears to be failing because the Microtronix Extension is not passing the "--device=2" option to the quartus programmer, although it is trying to download my flash programming utility design. I've verified that this info is in both my system PTF file as well as the target board system PTF that I created when I ported the flash programming utility.

Also, I can use the NIOSII IDE Flash Programmer to download this file to my flash successfully, but I don't think this is doing everything that is supposed to be done by the "Upload" command. And I'm pretty sure this won't be useful for the file system that I need to do next either.

So, where is the script or whatever that gets launched when you select "Upload"? Is there a manual set of steps I can perform to Upload vmlinux.bin myself?

Thanks,

Mike