D3s do tend to have a lag but mine was greatly improved by the enhancement program. There have been instances where this did not take, a re-flash will not fix and it has to be stripped and re-loaded, dealer will not want to do this without OK from LR as it is a long process. 
I had some corrupted files which caused problems too as wll as cold starting issues. Files replaced and fixed.
Recently a fuel preeure issue TSb was carried out which made an improvement in performance.
The lag is more asscociated with the auto box rather than engine there will be times when it will find itself in the wrong gear and will not kick down as you learn how the box works and the box learns your driving style things will improve. The re-flash may have set the box again and you are back to square one.
A few folks on th disco3 site had the same issue, suggest you stick a post on there and see what solutions they found from the dealers.
Here are some to get you started:
DISCO3.CO.UK - View topic - Acceleration hesitation at rolling stops
DISCO3.CO.UK - View topic - Throttle delay
DISCO3.CO.UK - View topic - Automatic transmission hesistates when changing up into 2nd!
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