The install errors come when it fails to register the message DLL. I do not have enough windows knowledge to understand why sometimes this works but mostly it doesnt.
You can set the heartbeat time to 0 which disables it.
The configuration is held in the registry under HKEY_LOCAL_MACHINE/SOFTWARE/Cheshire Cat/Nagios
You can export all or part of this to a .reg file and then import it - often people do this for the filters.
You can also do a scripted install; there are a bunch of options to the install exe -- it is created by Inno Setup and their documentation is here:
http://www.jrsoftware.org/ishelp/ look under 'Other Information', 'Setup command line parameters'.