I'm trying to make vanilla cupcakes from scratch and the center is always sinking in and when I touch them they're soft like they're under-cooked?
Maybe it's the all-purpose flour that I'm using? I have no idea..
Oven temperature gauges are wildly inaccurate. So it is very likely your times and temperatures are off. It sounds like the cupcakes are under-cooked, and are sinking as they cool. Use a good digital thermometer to test the internal temperature of your cupcakes. Shoot for 205 - 209F (96-98C) internal, at the center of the cupcake. Alternately, you can use the low tech. method of testing them with a toothpick by dipping into the center. If it comes out clean, they are done. If there is batter sticking to the toothpick, keep baking. ...and it doesn't hurt to have a good oven thermometer to see where your oven stands in terms of accuracy.