global_prefs.xml looks weird. It has each of the three limits occurring twice. I wouldn't have expected that.
global_prefs_override.xml looks better on paper, but the values there really just mean "accept the web settings", as far as I understand.
(global_prefs.xml reflects what the client read via scheduler requests from the web settings, from the latest consulted project AFAIK. global_prefs_override.xml shows what was set locally via boincmgr's advanced view computing preferences.)
Try this: In boincmgr, set
[x] Use no more than 1000 GB
[x] Leave at least 10 GB free
[x] Use no more than 90 % total
If you make all three limits explicit there, then we can be sure that any web preferences at any of the projects to which the client is attached to are ignored, and these locally configured limits are honored.