Samir this is what i was fighting, i have not been able to re-produce fully since switching to portable.
im guessing the installer just never overwrote them. the dates say the files are newer but it seems to just not link itself correctly
Im not sure this will help but somthing to note if using the installer on the pre-release Versions of win 11:
in my case windows defender was blocking the files Without notifying at all, but defender was changing the dates itself without an update to the file (metadata was updated).
so the metadata got updated but the contents of the file did not, and lua sees that as a new file either way apparently... and the installer is in the dark but still sees a changed file, resulting in no errors to the user.
from what i could see when i tried updating numerus times; that may be where defender is being an issue after its been fixed in Defender once it never happens again either, i cannot re-produce this issue anymore on win 11; 25h2 (26200.8457).
Oh i will also note i did re-install studio FIRST and after as well, it seemed to have no effect with my issue; even the command line could not run scripts with modules / extensions