Now I don't know if it is your mod or the other, but the travelling spidertron has default spidertron inventory size.
I have another mod active that expands the spidertron to 140 slots (https://mods.factorio.com/mod/spidertron-grid).

And whenever I get on a train 60 slots just vanish (back to the 80 slots of the travelling spidertron). Excess items just vanish into the void (and not on the ground like if you replace a larger chest by a smaller)
The equipment grid however is taken over from the other mod so it might be a prototyping order issue or something.

As a workaround I disabled show spidertron on top of vehicle and this fixes this issue (but of course does not show spidertron on top anymore)

Thanks for the report. It is an easy fix for either mod to implement, so I've just done it. Should be fixed in v1.4.11, and generally more robust to other mods messing around with the spidertron prototype.

The equipment grids worked fine because the spidertron prototype only contains a named reference to the equipment grid prototype, so when the other mod modifies that equipment grid, the travelling spidertron is still pointing to the same grid prototype.

I'm glad that the workaround worked as intended :)

Thank you for this very quick fix.

I can confirm it works, and I can have the spidertron back to sitting on top of a train.