What exactly do you mean by “database”? The database table modx_lexicon_entries? This database table should only contains entries that were changed manually in the manager.
I can’t reproduce this issue. When I install MODX 3.0.6-pl, the output in the package manager is correct.
Using dev tools here. Cache is cleared on each request.
I was under the impression that the entries in the lexicon files would also appear there but OK.
The only thing I can think of is I did try to install an addon called PageBlocks which doesn’t work with MODX 3 it seems (would be nice to know that before install) so had to manually remove some of that. Maybe there’s something left there though that’s influencing this though I did remove the plugin which should prevent any script injections.
This was all to try to devise a docker build and deploy system anyway, nothing more, so not the end of the world.