A couple of possibilities to check:
formatOtherKeysformatOtherKeyswas added in patch #235 ("xterm -v" should show at least that).- the different environment likely has different keycodes underneath. You might see some differences using
xevfor the combinations you want to use.
Your question did not mention the requisite resource setting for modifyOtherKeys. The formatOtherKeys resource alters the control sequences used by modifyOtherKeys (and you may have overlooked this in reusing the settings on a different system).
For instance, I can use this (on a different system...) to display the modified keys:
xterm -xrm '*modifyOtherKeys:1' -xrm '*formatOtherKeys:1' -e cat -v