I have an assembly program that shows a successful mate in the feature tree. However, the model window shows otherwise.

In the image attached, I have one of the two mates in question open for editing. My goal is to mate the center of the hole of the floating end of the piston to the center of the pin at at the base (where the blue line is). As you can see from the image, it shows that the axes are aligned, so SolidWorks internally knows that the mate is valid and has been applied.

I have tried manually rebuilding the document several times, and the program calls ForceRebuild3() and GraphicsRedraw() 3 times each. I also tried WindowRedraw() without success. In all cases the window does not (correctly) update.

It should be noted that if, after the assembly program completes, I select any of the pistons in the assembly and drag (same thing as "Move Component") even slightly, the two pistons in question snap into place. However, the program inputs the generated step file of the assembly into another process, so the user can't be asked to move around components in between the assembly and step export stages.

So.. SolidWorks' feature tree shows that the desired mate was indeed applied, but the model window does not reflect it. Have others experienced this? Are the commands I'm using wrong? Is this a known problem? I'm trying to determine these answers first before asking SolidWorks themselves.