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Part of the problem could be due to it being on an embedded operating system. The cRIO with embedded operating system is intended to have projects deployed to it and is not intended for use as a development system. We suggest using another computer as the development machine and deploying the project from there. I cannot guarantee complete development functionality on the embedded operating system. You could try reinstalling LabWindows/CVI, but the problem seems to be more related to the ActiveX libraries.ng systme limitation.
I will try to uninstall and install CVI but I believe that part of the problem may be not in a corrupted CVI installation but in a corrupted Windows installation. I believe that because there have been some problems with previous installations.