I was having the exact same issue,
Forge Mod Loader has found world ID mismatches
ID 19407 (ModID: BuildCraft:Transport, type buildcraft.transport.ItemPipe) is missing
ID 19406 (ModID: BuildCraft:Transport, type Buildcraft.transport.ItemPipe) is missing
ID 19408 (ModID: BuildCraft:Transport, type Buildcraft.transport.ItemPipe) is missing
ID 19409 (ModID: BuildCraft:Transport, type Buildcraft.transport.ItemPipe) is missing
etc.
I thought I'd just backup the old one and start fresh to see if I could get it to work, but even using a fresh world/config/everything for the 0.5.2 server the same message still pops up. I also looked in both my old buildcraft main.cnf and the updated one, but neither has a reference to any of those ID's.
I'm fairly inexperienced myself maybe I'm missing something obvious, but seems like these ID's are missing from the server update.