Are you using any WHERE condition in your LOAD script that may reduce the number of records eventually stored in the QVD file? Does your ODBC driver or your database some fetch limitation so you have reached the maximum number of records the user or the driver can get?
Does any other query to any other table return a supposedly different number of records? Do something like the following to create a counter field in your script, so you can easily check the higher number:
RecNo() AS Counter;
SQL SELECT *
Once you have reloaded the script, create a text object and use the Max() expression to see the highest value in field "Counter"
Do not any STORE for the time being. Does that return the expected value?