Got a really strange bug for ya, jopojelly.
Using Tmod (v0.9.0.2), Thorium (1.2.13.4), Simple Auto Chests (v0.3.2), and Boss Checklist (v0.1.1.3), my friend and I experienced some strange issues in multiplayer.
Using the 3 mods we had generation issues around the lower caverns that stopped world visual generation and caused Thorium items to drop from dirt blocks or any mob. An example is when killing ocean biome mobs they would drop Shadow Master's Treads in stacks. And shooting a Thorium Danger Dual-shot bow would yield Thorium items to drop from the arrows generating.
When using BC and Thorium, and not SAC, the world generation was perfectly fine but the item ID issues persisted.
When Thorium and SAC were used, and not BC, nothing was wrong whatsoever.
Originally when this happened I tried to break a block when the world generation got messed up below the caverns and Terraria crashed. The primary error was "index was outside the bounds of the array"
Oh, and I initially reported the ID issue to Thorium's developer, via his topic, and he said it was an ID desync likely caused by "a mod you've installed, how you're running the server, different mod versions downloaded or different machines."
I hope this is enough information to figure something out.