Only thing it could be (in my head) is that maybe the latest version of Xenia might incorporate the patches and adding the patches might do the opposite. There was mention that this might happen at some point, but i'll have a look into it...

Ok, the offical Xenia does not work with patches. Download Xenia Canary "github.com/xenia-canary/xenia-canary/releases" and add your patches into that folder. If they work it will say [patches applied] in the top bar. Rememeber to apply all patches for Perfect Dark with "is enabled = true" instead of false.

@@scottishserenityThe Canary build sorted it out, thanks for all your help

The N64 perfect dark decompile project runs really well on steamdeck. It is high Res and 60+ fps. Use the windows version as linux version seems to lock up on steam deck. I guess one advantage of the 360 remaster is high Res textures. But I'd struggle to tell the difference.