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If your application/script will run at all, it's not a dll problem. If they fail on startup, it may be something to do with the dlls. I had to replace all the references in my compiled applications when going to .2.2, as the dlls are all different and the previous ones (from .1.x) are not compatible with the .2.x release.
Input past end of file error was caused by an empty txt file that the script uses as an input. The affected scripts use icdb2bom.exe. I had only XENTPVX.2.2_esdm_win64 package installed when getting the errors. This package didn't have icdb2bom.exe and learned from Mentor it's included with Design Capture release.
Installing the Design Capture package after XENTPVX.2.2_esdm_win64 did not work so I uninstalled everything then installed in the following order:
Everything now works great!