I have been contacted by Microsoft regarding this issue (it appears that mIRC may have been one of the most active projects using Agent) and can confirm that this is not an mIRC issue.
mIRC does not require Microsoft Agent to work. mIRC looks for Agent on startup and if Agent is not installed, all Agent-related settings in mIRC are disabled.
The problem appears to be that Windows 7 assumes that any application that tries to load agent is a badly designed application that will crash if Agent is not present. So it reports this as a potential error, even for well designed applications that cleanly handle this situation.
This is unfortunate because it means that mIRC cannot test for Agent using standard methods under Windows 7 and will have to use a kludge to check whether Agent is installed for users who wish to continue using Agent under Windows 7. mIRC will continue to use the standard method under all other versions of Windows.