Yes, this is indeed something that happens to orbitals that only have speed 1km/s occasionally. I once lost a fully loaded fighter training hangar base (no fuel loss when inside immovable base) this way. Well, actually it didn't vaporize, but it randomly teleported into the sun, and I could draw it out with a freighter, but some years later it happened again... .
The solution to this is to include at least one single tiny engine on your orbitals, so their speed equals to something larger than 1km/s, and then the error will never appear anymore. Doing this costs you nothing still, and it is well explainable to have some "maneuver jets". (maybe to protect exactly against slowly falling into the sun after tiny accumulating orbit destabilizations?
)
It is neat anyway for fuel bases specifically to have some speed of maybe 10 km/s or so, which enables them to fly to the closest moon of their gas giant, so they can unload their fuel there, and tankers can make their own schedule while your log stays free of the "harvester over 90% full" spam that occurs otherwise.
