There are some inconsistent behaviors regarding fuel lines. E.g. After turning the Fuel Line option on for a central tank, then adding auxiliary tanks to its surface, I usually have to detach and re-attach my engine to get the game to recognize there should be fuel in those side-mounted tanks.
Other times I have to manually turn off Auto Select Fuel Type and select Kerolox, after which point the setting seems to stick (i.e. I can turn it back to Auto and Kerolox remains selected).
Sometimes even with a ton of mucking about it’s difficult to get the engine to utilize the fuel (even after confirming intervening parts are all connected by via “fuel” type connect points) – then launching/reloading the craft magically seems to fix it.
I haven’t thoroughly investigated all the corner cases, but the core problem is pretty easy to reproduce by:
a) create a new craft in the build editor,
b) add a fuel tank on top of the Command Disc,
c) add an Engine below the Command Disc and note the Delta-V displayed in Staging Analysis,
d) add another Fuel Tank, to the side of the first one,
e) turn “Fuel Line” on for the central tank and command disc, and notice the Delta-V has not changed (and the side-tank is still empty),
f) detach and re-attach the engine and observe the side-tank is now full and the Delta-V has gone up.
An alternative to (f) is manually toggling the fuel type on the side-tank then setting it back to Auto.
This behavior tries to account for players adding side boosters and is intentional. There are some edge cases that can be frustrating, but the side boosters seemed to be the most common use case.