If the rafts appear correct…and the supports appear correct up to the point they ought to connect to the model- then My money is on the model.
Just because it says its manifold is no guarantee it qualifies as Solid.
manifold modelers are surface modelers.- they were optimized to facilitate CNC Milling operations in which a surface needs to describe the bounds of a volume- but does NOT have to be solid, because the mill head is simply tracing a spline in space- which side of that line is solid material and which is not depends on which side of the spline the cutting head is on.
In surface modelers a surface has only ONE side- and zero thickness. So imagine a cardboard box where the sides were not actually part of the same sheet of cardboard- just six square planes arranged in a cube. They each only have one side- but all the sides are facing out.
Because the six sides describe a closed volume- even tho not connected in a single surface, this model would still qualify as Manifold.
If one side was missing, it would be Non-manifold. But also if any of the sides were displaced to create a gap between their edges and the others, that would also be non-manifold.
A surface model- that has, say, One spline between two patches that is NOT stitched may export into STL as having contiguous points along that edge… and those point NOT being connected in both directions as required of a solid model. That would be a model that is manifold- but NOT solid.
There are so many independently written apps and algorithms out there for converting one kind of geometry to another, that it is really common for geometry to get corrupted.
Check the STL for solidity- or look at your export functions to see if alternate settings net you a more reliable model export.