As described here: Chicken-Bones/ForgeMultipart#96

Notice how the person use anchors. I have a similiar issue, but with another mod. "Tubes!" .

When I place the Tubes, and then surround them with FMP microblocks, and place the World Anchor, and then restart the game, all the tubes and microblocks vanish.

If I do exactly the same but instead of using World Anchor, I use Chickenchunk, it works just fine.

I'd like to use the World Anchor thought, cos it consumes fuel and is thus balanced. It also has a cart version of it.

Considering Railcraft Anchors are essentially the "reference implementation" of a chunkloader, I'm going to have to assume this is a case of CB doing hacky stuff in FMP and fixing his chunkloaders with more hacky stuff.

Try some other chunkloaders besides these two.