Hi again,
If found the problem of the above described behaviour, and it has nothing to do with Stardog.
The program which iterates over the different ind's had a memory leak.
And (bad practices) I was running the Stardog database on the same cluster as this program.
So the total memory was getting critical (which resulted in Stardog providing such logs).
Fixed the leak, and ran Stardog on a different node solved the problem.
Kind regards,
Bram