What size magnets do you use, and where do you get them?
I just buy them off of ebay. They are size: 1/8" x 1/16" or 3.2mm x 1.6mm
Sometimes people round off the mm when listing them, and just say 3 x 1.5 - when they are really 3.2 x 1.6, while other times they actually are 3 x 1.5, so sometimes it's best to ask to make sure they are the same size as ones you are using.
I don't know if this helps people, but this is how I make sure that all magnets are facing the correct directions for objects to connect properly:
I glue my first magnet hardpoint onto a mech. Then I stick a second magnet to the first magnet, and glue the weapon onto it's end. This makes sure the two magnets will attach to each other. When the glue has set, I can pop off the now magnetised weapon, and repeat process to magnetise more weapons. To make sure all hardpoint magnets on the mechs are facing correctly, you just take a weapon that has a magnet on it, and stick another magnet to the one on the weapon. Then put glue on the second magnet, and attach the weapon to the mech where you want a new hardpoint to be. Once the glue has dried, the weapon and its magnet comes away, and a new hardpoint magnet is now on the mech, correctly aligned.