I have tested this version extensively these couple of days. I gotta say, it's the best version I have tested so far, and the workaround is brilliant.Should be fixed in 1.4.4.
That being said, I still get some incompatibilities with some DLC, where it says it installed successfully without there being any new content, while installing them through BBM/devmenu works mine.
I know you said that you are using the standard known method for installing, but I don't know man, something is definitely off.
Either way, great program. Thanks a lot for all the time and effort spent on this program