As described in the title, sometimes the beams will be invisible: In my case salvage beams were properly mining but were invisible. The personal mining beam (when in EVA) was invisible too. When I switched to cannons to see if other particle effects were affected it crashed my local server. Restarting the game solves the problem.
I couldn't locate anything in the logs about the beams not showing up.
I think this is where the cannon crash happens in the logs:
[2016-05-22 15:23:14] Client received paratresized command RequestServerTime[void], packet 12056
[2016-05-22 15:23:14] Exiting (normal) because of exception java.lang.NullPointerException
[2016-05-22 15:23:14] java.lang.NullPointerException
[2016-05-22 15:23:14] at org.schema.game.common.controller.elements.ProjectileController.getPhysics(SourceFile:541)
[2016-05-22 15:23:14] at org.schema.game.common.controller.elements.ProjectileController.update(SourceFile:818)
[2016-05-22 15:23:14] at obfuscated.abg.a(SourceFile:2284)
[2016-05-22 15:23:14] at org.schema.game.common.data.world.Universe.updateSector(SourceFile:1079)
[2016-05-22 15:23:14] at org.schema.game.common.data.world.Universe.update(SourceFile:1111)
[2016-05-22 15:23:14] at org.schema.game.server.controller.GameServerController.update(SourceFile:1284)
[2016-05-22 15:23:14] at org.schema.schine.network.server.ServerController.run(SourceFile:270)
[2016-05-22 15:23:14] at java.lang.Thread.run(Unknown Source)
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down element collection thread
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down pathfinding threads
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down universe
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting segment request thread
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down simulation
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down active checker
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down sysin listener
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down mob thread
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] shutting down game map provider
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] Stopping to listen!
[2016-05-22 15:23:14] [SERVER] Stopping Listener
[2016-05-22 15:23:14] [SERVER] Stopped Listener
[2016-05-22 15:23:14] [SERVER][SHUTDOWN] disconnecting all clients!