Once you take the hand load perk and use reloading benches to make hand loads you are unable to switch from say a match load to incendiary rounds with the AMR .50 cal? I have also notice this with .308 and 5.56 rounds used in any weapon that can chamber those ammo types. Once you have used a hand load, even if you do not have that ammo type in your inventory you are still unable to switch ammo from whatever is in the clip at the time. When you open your inventory and click on a new ammo type the filled bullet point remains next to the already chambered ammo type and all you get is a clicking sound, the animation of changing magazines will play when you close your pipboy but that is it...
The only way I have found to get around this is to drop all ammo except for the type you want to use, change weapons, change back and then reload. So to change to AP rounds with the sniper rifle I first need to drop all standard rounds, all hollow point rounds, and all JSP rounds, change to a different weapon and then back to the sniper rifle, go into inventory and load the .308 standard ammo, pick up all of my other ammo and then I can continue to play.