Why are you using a repacked region free cia? The CFWs of today you don't even need to unpack-patch-repack the cia for region free, they use loader replacement to enable region free (for both cartridges and cias). With the updated CFW you can download the usa/jpn/whatever-region cia from Nintendo server and install it and they will work just fine.
IF Luma3DS has a bug that it cannot install region free patched cias, it's because no one cares to use this method anymore, since with loader replacement we don't need to do that anymore.
"IF" because you never said that you tested with other region free patched cias. So, it's impossible to know if what you are said is scientifically true, since you didn't use the scientific method to know if it's a Luma bug or the repacked rf patched cias that you are using bug.