it seems to happen with some registry locations when you append letters.
my escort has the same registry number as my sci vessel with an a appended, and while it shows the proper info on the saucer, the hull sides have the same 9870 repeating number sequence on them instead of the registry number.
Hey guys and gals I found a quick work around for this bug, If you select Vesper from the regular menu not advanced the registery appears right although highlighted in red, then you can go into the advanced settings and change the rest of the parts to your likeing, however just make sure to leave the saucer set as vesper or else it bugs again. You can however change the design of the hull markings with no ill-effects to registery.
The only downside I have seen to this method however is when its done the secondary hull reverts back to standard colors and no ammount of changing colors seems to fix it. Hope this helps