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So I figured I'd come back and share what I learned. 

Create_Capture() wants to use the S_STD IOCT to set the device to a known standard something like NTSC 30FPS, PAL 25 FPS, 1080I 30 FPS, 1080P 60 FPS, etc there are bunch of them but they are all discrete values that are tied to analog, broadcast or DVD, BluRay video standards for a camera module like the MT9P031 many of these could apply but the module can do much much more, specifically it could do full 5mpix capture at 1 FPS if you wanted and there is no standard for that. 

To complicate things further whomever implemented the MT9P031 driver didn't setup it up to work with the S_STD IOCT, they could have but they didn't, I can kind of sort of understand why they might have done this but it would have been nice for them to do it as it isn't too hard. I figured out how do this by setting the v4l2_input.std field for the mt9p031_inputs structure in {kernel}/arch/arm/mach-davinci/board-dm368-leopard.c 

/* MZS MOD added MT9P031 std bit filed and set it in the struct */
#define V4L2_STD_625P_50|V4L2_STD_720P_30\
     |V4L2_STD_720P_50|V4L2_STD_720P_60\
     |V4L2_STD_1080I_30|V4L2_STD_1080I_50\
    |V4L2_STD_1080I_60|V4L2_STD_1080P_30\
    |V4L2_STD_1080P_50|V4L2_STD_1080P_60)
/* Input available at the mt9p031 */
static struct v4l2_input mt9p031_inputs[] = {
	{
		.index = 0,
		.name = "Camera",
		.type = V4L2_INPUT_TYPE_CAMERA,
		.std = V4L2_STD_MT9P031_STD_ALL,
	}
};

This allows the S_STD IOCT get a little further, however there is another problem the vpfe_capture implementation of the S_STD IOCT calls vpfe_config_image_format() which
attempts to call the g_fmt operation handler on the sub-device (in this case the MT9P031 driver), however there this driver doesn't implement the g_fmt operation which would be ok
and the function should fall back on some defaults but the logic here is very bad and it ends up trying to setup the ccdc with an uninitialized stuct and everything fails.

 (see this thread  http://e2e.ti.com/support/embedded/linux/f/354/t/182860.aspx)

To fix this I eventually ended up adding this line just before calling the g_fmt operation so that the defaults will get used if g_fmt fails or isn't implemented. 

 sd_fmt = vpfe_dev->fmt;

After this the DMAI Create_Capture() function finally works and Capture_get() and Capture_put() work but that's as far as I got because I realized that this interface just isn't going
to be flexible for me and I'd have to write the capture part of my application using IOCTL calls. 

I hope this info helps someone else down the road. 

Matt S. 

I've been using the RidgeRun SDK which handles the kernel config file for me you and I haven't had any problems with it finding the MT9p031. 

You may already know this but this may help, you need to have the "cpfe_capture.interface=1" in the kernel boot arguments, this lets it know that you are dealing with the MT9P031 instead of TVP5146, apparently the 2 share the same I2C address. There are some comments about this in linux-kernel/drivers/media/video/davinci/vpfe_capture.c

I put a copy of what I think is my kernel config file ".config" here http://pastebin.com/7iFFbSpy

I took the time to get KGDB -> GDB debugging working with my board and it has been invaluable for figuring this stuff out. 

I hope this helps. 

Matt S.