Sixteen configurations? Be very, very careful.
I feel your pain. During a rebuild if SW can't figure out all the mates rather easily it will fault out and either suppress some or just ignore them.
Some tips that have helped me: (Are these mating tips? Ooo boy!) First, depending on what your settings are, when you establish a new mate, SW will assume that mate is suppressed in all other configurations.
Learn to use the "Configure Component" or "Configure Feature" tool. Pick an item in your feature tree, right click, and select "Configure Component". You will see a spreadsheet style dialog box that allows you to select which configurations that feature is suppressed in. You can even do some spreadsheet style commands in there, like Copy and Paste, etc. Do this for every new mate or feature as you create them and it can help.
Minimize the number of mates. Less mates = less confusion. If I use a parallel mate to orient a part and then later set a distance mate, the parallel mate becomes pointless and just causes SW to have to calculate that much more. Another chance to blow up. Delete unnecessary mates.
If I'm mating a part to a bolt pattern I will only use the concentric mate ONE time. A part should not need more than three mates to fully define its position.
Avoid advanced mates if at all possible. They're nice but they're trouble. We fell in love with the Width mate that allows you to center one part on another. But my my experience since then has taught me to avoid it if possible.
I have recently started to see the wonderful advantages of using Planes, Temporary Axes, and sketch elements as mate elements. Example: two parts will always be centered on each other as their sizes change. Don't use the Width mate. Build the parts correctly (using Mid-plane Extrusions a lot) so that the the critical planes remain at the critical operational points. Then you just mate the center plane of one part coincident with the center plane of the other part, and set it to unsuppressed in all configurations. A simple coincident mate is less likely to blow up on you than a complicated Width mate.
Another example: you want the axis of a cylindrical surface to be parallel to a flat surface. Turn on Temporary Axes, and set the parallel mate. Its simple and reliable.