You could be saturating the smaller choke's core, even though it has
a higher measured inductance, or, if it has a larger form factor than
your choke, perhaps it is your choke that is saturating and that is
the desired operating mode.
OR, it could be related to the wire size used in each case.
The permeability of the core is/can be a big factor as well.
The single LC filter setup at the front end of the main rail should
be enough (my not even need two chokes). Perhaps some storage
capacitance near each sub-circuit, but not likely to need a full on LC
filter.
