Some stencil fbo code runs on ati but not on nvidia

yes, it looks like it is a remaining problem. these topics have some info on how it is usually handled;

according to second topic, method of blitting i supplied to you hereshould work

also, just blitting stencil buffer doesn’t work for you? you may report it to amd, to remind them.
you can send a test case to devrel@amd.com (with pierre.boudier@amd.com in CC)