I have a typical 6" Z table setup however on the side i have a trough where i have my indexer setup in the X axis. This allows me to go down an additional at least 6".
My springs stretch, everything seems to stay stable and i don't seem to have a problem mechanically or software settings-wise with my range of motion. I don't recall that we had to modify the normal settings for the table to make it give me the added movement.
I would suggest a direct email to Shopbot since yours is not a typical setup you may be exceeding some type of built in limits to the software
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