I can not get the chunkloaders (v.1.0.6) to chunkload after a server restart using Forge 12.18.2.2122. It seems I have to manually go there to trigger chunkloading

Oh boy... let me go take a look and see. Do you have any run-time logs (your FML Server-Latest.log file) I could take a look at for reference?

So I've just updated all of my mods to Forge 2125 and am testing in my dev environment.

I'm not seeing this bug at all; have you tried re-placing all of your Chunk Loaders and seeing if that's a persistent issue then? Sounds like PersistentBits is having a problem with your Serialization file (the PersistentBits.dat file). And I know that on my server (running 2121) they work fine.

The reason this should work has nothing to do with the Chunk Loader needing to be re-placed. The way my mod works is that when you place a Chunk Loader, it adds it to a List of chunk loaders and then outputs that whole list to the PersistentBits.dat file. So by breaking the Chunk Loader (removing it from this list if it can) and placing it again (re-adding it to the list), you should be good.

Let me know if the issue persists, but I can't imagine it can't be resolved by re-placing your Chunk Loaders.