When you have more than one select in a script and you use the Execute Scripts command, the execution stops when any one result set returns more rows that the Fetch Limit.
For example:
Fetch limit set to 1000 rows.
Select colA
from table_with_500_rows;
Select colA
from table_with_1500_rows;
Select colA
from table_with_500_rows;
Select colA
from table_with_500_rows;
Running this with the Execute Scripts button, you will get the results from the first and second select statements (up to 1000 rows), but then execution stops.
This is on version 7.0.3.37 64Bit.