If filled with water and I reset the game they reset to individual blocks. You might want to have them block update on game start to reform the multiblocks.

Was this right after updating to 1.4.3?

Updating from older to 1.4.3 will make that happen yes, see this:http://minecraft.curseforge.com/projects/agricraft/files/2263798

IMPORTANT: in this build the multi block code for tanks has been completely rewritten from scratch. This means a lot of issues have been resolved and performance should be better now. However this also means that multi-block tank structures in existing pre 1.4.3 worlds will break. BACK UP YOUR WORLD BEFORE UPDATING! To fix this, you will either have to manually break and replace one block for each of your tanks, or break all tanks in your world before updating.

I'm closing this for now, if it occurs again, feel free to reopen.

Could have been earlier. Discovered it after updating to 1.4.3.