Cygwin conflict

I have had the cygwin tools installed on my PC for a long time. I installed the Nios II IDE after installing the cygwin tools, and have also successfully used the Nios II IDE for some time.

Just yesterday, I uninstalled, and reinstalled cygwin. Now, I cannot build anything in the Nios II IDE, not even the "Hello World". I am sure that the external cygwin tools are somehow affecting the Nios IDE operation, but I can't pinpoint how. Any ideas?

Things I have tried:

-- Uninstall and reinstall Nios II IDE (hoping it would rewrite whatever crucial environment variable is missing)

-- Checked my path environment variable, and I don't have cygwin in the path

-- Rebooted a couple of times for good measure

Error that I get:

**** Incremental build of configuration Debug for project hello_world_1 ****

make -s all

"X`which cygpath.exe 2> /dev/null`" was unexpected at this time.

c:/altera/kits/nios2/components/altera_hal/build/app_rules.mk:152: `: No such file or directory

... (lots of similar lines til build fails)

--Tracy