Milling toolpath not covering desired areas

[cdespinosa2ZCF4]

My project is two pieces, milled on both sides; I have two models (Base and Riser) that correspond to two Manufacturing Models, and each model has two setups, First Side and Second Side. I'm milling on a Snapmaker 2.0 A350 with a 1.5mm flat tool.

The Base came out well, exactly what I wanted, but the alignment when flipping the piece over to mill the second side wasn't exactly perfect, so for the Riser piece, I want to mill locator holes in the stock around the model. 

My problem is that when simulating the toolpath for the first side of the Riser piece, it's just not covering three places: it's not milling any of the locator holes; it's skipping about half of a big area at the bottom, and it's not milling a recess in the middle of the piece at all. A similar slot and recess on the Base piece came out just great with the same setup, machine, and bit (I literally duplicated the setup for the second model).

The areas missing are circled in black on the screenshot below. The locator holes are 5mm in diameter, plenty wide enough for the 1.5mm bit, and the slot is the same with as the slot that was milled successfully in the Base model.

Any suggestions on how I can diagnose why the toolpath generation is not covering these three areas?

[seth.madore]

Would you be able to share your Fusion file here?
File > Export > Save to local folder, return to thread and attach the .f3d/.f3z file in your reply.

[cdespinosa2ZCF4]

Here's the .f3d file. I am only using the one pocket clearing strategy on the setup. I haven't learned whether, when, and how to use multiple strategies per setup (I'm pretty new to Fusion specifically and 3D milling generally, I've done a fair amount of 3D additive printing and 2D CAM on the Snapmaker using Shapr3D and the Snapmaker Luban tools).

[seth.madore · Accepted solution]

I think the issue you're running into is that you've selected the top level of the MFG Model, and it's actually grabbing everything that's in there, including both the riser and the base: