I recently tried to build the game I'm working on against SDL hg and I noticed the renderer clipping is totally broken or at least it doesn't work any more as it did in the latest SDL stable (2.0.3).

I wrote a simple test program to verify the problem wasn't in my game, you can check it out here: http://pastebin.com/WX9tq7rk

You can see the results of building the same program against SDL 2.0.3 and hg here: http://imgur.com/a/8pDrD

After noticing this bug report: https://bugzilla.libsdl.org/show_bug.cgi?id=2927 I hacked the code a little to find out the patch derived from that report is causing the problem.

For example in SDL_renderer_gl.c replacing
 data->glScissor(renderer->viewport.x + rect->x, (h - renderer->viewport.y - renderer->viewport.h) + rect->y, rect->w, rect->h);
with the old code
data->glScissor(rect->x, renderer->viewport.h - rect->y - rect->h, rect->w, rect->h);
Fixes the bug.

I don't know if the problem is in that particular line of code (and in all the similar ones in the other renderers), in SDL_GetRendererOutputSize or in the viewport, but hopefully this will give you a starting point to investigate the issue further.