I've not quite got the same problem but I'm also looking for any reason why the rebooter option in WiiGator's Backup Launcher 0.3g and NeoGamma doesn't seem to work properly since I updated from 3.3E to 4.1E. I've tried using DOP-IOS to download a patched IOS36 and it hasn't made any difference.
Basically the rebooter option allows the backup discs to show in the Disc Channel but I get the black screen with "An error has occurred..." message if I try and run them. I've not used it for a while because it was broken in some of the recent cIOS249 revisions but rev14 apparently fixed the rebooter so after installing it and updating from 3.3E to 4.1E I thought I'd try it again.
It's not a major problem since they'll load fine if I don't try and use the rebooter option but I'm just curious why I get the error message? I'm assuming I need either need older or trucha patched IOSes but I'm not which ones in particular. I tried using a much older version of cIOS249 and just get exactly the same problem so the issue is definitely related to me updating the firmware (which I only did after reading all the "it's totally safe now" threads).
[EDIT] Just for clarification, I had cIOS249 rev14 installed (nothing else, definitely not CIOSCORP!) and did an update via Nintendo (not using Wanin's updater as I just wanted to get a full update without needing to patch or skip anything)