I haven't been able to duplicated any of this. I just now deleted my homecoming.exe, and it was replaced by Island Rum after a rescan.
What I can't see is if you're using a different manifest than I am. I'm using http://patch.savecoh.com/manifest.xml - I don't know if that's the official one, because these forums here don't list the official one anywhere, but the URL I use does show what appears to be a correct manifest.
I also can't see which path you have selected for Island Rum to write the files, or if you're using a non-admin user that has no rights to write to the folders inside the CoH application. The files (including homecoming.exe) might be getting written to some completely unexpected location, or failing to write at all. Island Rum is not capable of asking for administrator rights, because an unsigned app that downloads stuff and then asks for admin rights will make Gatekeeper very upset.
And lastly, the download locations are out of my control, and I can't do anything about failed downloads. I see in the manifest that homecoming.exe is only available from one download site, and if it's not reachable for you, that would definitely make it impossible for Island Rum to get the file (IR doesn't do proxying or any sort of bittorrent-like behavior, it just downloads via http).