I'm honestly not sure of the quality of what I was smoking at the time I made that function, but it must have been better than what I have now.
That function is working as described, and I think the mixup here is that I created this for some other purpose entirely and misrepresented what it actually does.. That, or maybe I created the function for your purpose but just didn't think things out very clearly, in fact if I did that, I made some big mistakes.. What this function does is adds the files to every single installer created, hence it is under the section that says "common options for all compiled installers" but the problem is that these files are added to \3rd Party Tools. I guess this would be useful for someone to pre-bundle their remote support software or another app with dSupportSuite, that couldn't otherwise be downloaded on demand. But it won't serve our purpose of distributing custom config files for those 3rd party tools...
First, what you need for patchmypc.reg and other config files, is to have them not just in the installer creation, but also in the config uploads -- which the function above does not do, it only bundles those files inside custom installers it does not upload them in configs..
Second, you also need patchmypc.reg in \3rd Party Configs not \3rd Party Tools.
Finally, you need patchmypc.reg in only select custom configs, not all of them -- correct?
Solution: You need to actually launch the dSupportSuite config for the given client ID or template you want to include patchmypc.reg in. Now go to the custom apps page. under the import config files(s) before running option, you would have of course patchmypc.reg typed into the box for the patchmypc custom app. That's correct. Now what to do with the .reg file itself is to click the browse button, when the browse window pops up, just copy/paste the patchmypc.reg file into that window. This will put the .reg file inside the config\3rd Party Configs directory for that client ID or template, and no others. now you can select it and all should be well. The .reg file will now be distributed both in custom installers compiled for that client ID, and also uploaded to dCloud with the config for that client ID.
Simple, not so elegant, but effective. The only pain in the ass is going back over all the client IDs you need to distribute that .reg file to, doing the procedure above for each one, and re-uploading the config. I don't have an easy answer for that part.