Well that is interesting. There actually are some tricky ways to get a little bit of vacuum from a non-turbo diesel intake manifold - or from any airflow. I think some Mercedes did some of that. It might just be enough differential pressure to work a tiny lift pump. And your
L4240 does happen to be from those years (2007 to 2013) when Kubota was experimenting with innovative intakes trying to beat the
Interim Tier IV emissions requirement.
I know about weird intake mods because we have a 2008 Kubota
M59 from that same era. It came with the most bizarre EGR setup I've ever seen. This EGR is a technical marvel involving a water cooled muffler and a device cantilevered off the back of the engine block with some extra intake manifold valving whose operation varies with coolant temperature - as well as a couple of pages in the shop manual dedicated to explaining how it is supposed to operate. BTW, thanks to Kubota for those pages; they saved me from having to take it apart to figure out what was happening in there...
So a vacuum operated lift pump in a Kubota from those years would be just strange enough to be in keeping with what they were doing back then.
If any of this is real - and there really is a vacuum lift pump - it might simply need a replacement vacuum hose.
Luck,
rScotty