Note: If you need my configuration again, I can email it to you.

I was doing a little more testing with mining, and found some more strange issues related to my previous ticket. But before that, I was using the following on my testing server:

CraftBukkit 1.5.2-R0.1 (I'm aware I'm a few builds behind.)
OtherDrops 2.8b542
CoreProtect v2.0.5 (This is a logging plugin. Should have no impact on mechanics.)
mcMMO 1.4.06-beta5 (Should have no impact on mechanics for my tests that don't include mcMMO. This plugin doesn't deal with any form of block (re)placement anyhow.)

I know I could make multiple tickets for this, but they're all linked to "ReplacementBlock" so I posted them all here.

Logging Issue:
If you break a block, and the block is replaced with another block, CoreProtect states that the block you just broke is the replacement one. Obviously, this isn't true. To clarify, let me provide an example:

You break an iron ore block, and it gets replaced with cobblestone. If you log the block to see who broke it, it will appear as "PLAYER" breaking one block of "COBBLESTONE" when it should actually be "IRON_ORE".

mcMMO XP Issue:
Because mcMMO also "logs", I believe the nature of this issue is similar to the last one. If you break an iron ore block, and it gets replaced with a cobblestone block, you will get xp for breaking a cobblestone block instead of the iron ore block. Likewise, if you break an iron ore block, and it gets replaced with an iron ore block, you will get xp for breaking an iron ore block.

(The following issues are a bit more specific, but I just wanted to write them down here for the sake of bug reporting.)

Mineral Duplication not limited to Gold Pickaxes:
Diamond pickaxes have a similar issue, when mining emerald ore, that gold pickaxes have when mining coal/diamond (I haven't tested gold pickaxes on emeralds or redstone). In other words, a diamond pickaxe can duplicate emerald ore in the same way that I found gold pickaxes to duplicate diamond/coal ore.

Lapis Lazuli refuses to be replaced by anything:
I have "replacementblock: COBBLESTONE@1" defined when Lapis Lazuli is successfully mined, yet, when I tried mining it with a gold or diamond pickaxe, it gets replaced by absolutely nothing. Maybe sort of like "replacementblock: AIR" but I'm really not sure if this case is similar to the last.

Netherrack@1 still wants to drop items:
I have specified "NETHERRACK@1" to drop "NOTHING", yet, when I mine it, it still drops "NETHERRACK". Not sure what's happening there. No clue as to the nature of this scenario.

Thanks for that. The first two are definitely related and I have some ideas for fixing. The last three also seem related but a different issue.

Please guys, fix this, my logs would be so much more lighter and easier to read. I can't disable Otherdrops since it is pretty essential to my server, same goes to Prism and both plugins doesn't seem to like each other.

I'm having exactly the same problem, aswell for the mcMMO xp issue (I've disabled xp from ores, since I'm using Otherdrops as an antixray, but if a player from my server wouldn't point that out people would be xperiencing all day long.
I'm not using CoreProtect but Prism, but it seems to be the same issue.
I've stripped my IRON_BLOCK break part to it's minimum and it looks like this:

IRON_ORE:
    - drop: COBBLESTONE

People can't break the Iron ore but still it is dropping cobblestone and sometimes also iron (the second part could be related to the way mcmmo works). Basically players can farm lot's of cobblestone and iron beeing in one place.

What is interesting unlike CommodoreAlpha's case the "blockbreaking" isn't logged in Prism, but I get a huge console spam everytime a user tries to break that ore.

It's not such a big issue for me since I have almost 100% ores replaced by stone on my map but I could guess that it is causing big issues on common servers, since using Otherdrops in such a configuration with this particular plugins on the server, is not possible.