The default R script works fine on the lists and in fact applying the R view to the list seems to reset the flag that disables the default R script on the query, because the default script works again if I run it on the query afterwards.
I think something in my code is triggering the issue. More specifically I suspect the issue is triggered by one of the functions that communicates with the server to retrieve, write or delete data, because everything runs smoothly until I add the last bit of code that uses getRows, labkey.deleteRows and labkey.insertRows. Each of these functions seems to work fine individually, but the issue seems to occur when I run them sequentially in the same script.

Thanks!