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I have not found any known issues with CVI 6.0 Distribution Kits built on Windows NT 4.0 and used for installation on Windows 2000.
I just spent some time with one of our test machines, and was able to successfully build one of the CVI 6.0 examples on NT 4.0 and install it on to Windows 2000 using the Distribution Kit. I did not encounter any issues during any part of the process.
I do not expect you will have any problems with building and installing the distribution kit.