I have the same problem, the relative speed makes no sense between my 2 vessels: KSS-1 and KSS-Mission2 As you can see on the video: Using the KSS-Mission2 their distance becomes bigger, switching to KSS-1 without changing anything (not burnout, nor rcs, just changing the vessel) the distance becomes smaller. What is happening is: the used vessel is the faster one.
KSP Version: 0.25.0 Build 00642 Linux 64-bit, KSP 64-bits and 32-bits (tested both) using Steam Save folder: https://www.dropbox.com/s/mtwo0mjlb8iuut5/Agustin.zip?dl=0