The Atmosphere code was modded to add again the code removed on commit 46a4357, for load KIP Patches using fusee.bin to load system.Dunno why loader ips patch works for you at all since it is a kip patch, and support for kip patches was removed with 1.7.0 release.
I load Atmosphère with Hekate's FSS0 method, so the code removed on commit 46a4357 code doesn't matter.
Also Sys-Patch should take care of that even if you are using the official Atmosphere, and on this case is not happening.