Vanir

Quite possibly, however it's definitely Kerbalism that is the conflicting component here. If I've got time I'll go through adding in every single mod one at a time, see if I can identify the point of failure.

Already checked that. With just a single Mk1 command pod on the launch pad, brand new campaign with default difficulty settings. Crew report yields 1-2 science which is stored in the pod with the kerbal, and then when I try to "recover vessel" no science is yielded. Nothing to do with staging or any science-storing parts being lost before recovery. I do have a fair few mods installed on top of kerbalism, however I've been through and disabled/enabled all of the mods which alter the science system to try and identify the cause, all to no avail. After disabling kerbalism the science recovery works correctly with the stock behaviour.

I can also attest to this. Trying to start a new campaign in 1.4.5, want to try out kerbalism for the first time as well. It's possible to transmit data, however any science stored in the vehicle is lost when recovered. Would love to see a fix to this @N70 as I'd love to get started on my new campaign asap!