I seem to recall that there was a change in QlikView Server that could be made to one of the .ini files to turn off the storing of metadata to QVDs. I'm not sure if the same is true of Sense. It's not ideal, as the information written to QVDs can be very helpful, but if you are hitting problems this could be the answer.
The lineage in the QVD should be just for the individual QVD being written, but it absorbs lineage information from prior QVDs if it is not clear that it is a separate load. If you load allows you to drop all tables between each QVD that might help, but typically that is not possible as you will be using a table to enumerate around.
The solution you have seems to be working. You may be able to do it in one script, if you ensure all tables are dropped between one part of the process and the other - but I don't know this for sure.
