A beacon requires a specific amount of blocks, so try putting them into seperate pyramids As said above
You don't need a separate pyramid for each beacon. Here is a picture of my set up. I also have 2 beacons. Also check out this picture from a wiki File:Efficient beacon.png – Official Minecraft Wiki
Do the following: 1. Open the Beacon Menu 2. If it doesn't let you select a beacon effect then do Step 3. If it does, skip Step 3. 3. Close the Beacon Menu. Go back to Step 1 4. Choose your beacon effect and add your iron/gold ingot or diamond/emerald. 5. Click the check and you have yourself a working beacon. Basically, just open and close beacon menu it until it lets you choose the beacon effects.
I am not sure why this problem occurs, but the same thing happened to me and resolved itself after a few days. I would just leave the beacons in place and occasionally check back to see if it allows you to set an effect. Also, is your pyramid solid iron? The 4 beacons that would not allow me to choose an effect for a few days had mixed pyramids whereas the beacon with a solid pyramid worked perfectly normally.
Sometimes with servers like this the menu of the beacon can glitch out very badly. You can break the beacon then place it down again and that should work. You can also break some of the blocks under the beacon then placing them back, or just keep opening and closing the beacon menu until it finally works. Hope I helped you with your problem.
A while ago there was also issues where on certain spots on islands you couldnt get a beacon to work and it never would. It was frustrating. Archiving.