The mineral manager is very annoying... half the time your ores get shot 10 blocks away because of the cobblestone that replaces the block. Most of the time it tends to land in lava for me. The text it gives you cloggs up chat and the cobble stone hides the other ores behind it.
I would recommend changing that plugin out for one that does a full server reset of all the ores like once a week.
While I agree that the way that Mineral Manager 'shoots' your ore out sometimes is annoying, and it can sometimes go through the floor, if there is an empty space beside the ore, this is less likely to happen. At this time, the ore placeholder is now mossy cobblestone for an easier identifier for when an ore is waiting respawn versus a tunnel with some work done to it. There is nothing that can be done at this time to disable the messages that are sent because of the plugin, which is something that was looked into the day we added the plugin to the server.
Adding a plugin to replace this that regenerated all of the ore in the world would be terrible. The biggest reasons for this is that it would crash the server while regenerating the ore, and this would ruin several different builds. Anyone that decided to build underground and had an ore in their structure's space would suddenly have floating or clinging junk in their build, and depending on what materials were used, this could cause a great deal of loss should someone who had a decorative diamond block have it replaced with coal.
To help your issues, I recommend digging around the ore that you are mining, and covering any nearby lava if you are mining something valuable like diamonds.
~Zaralith
