I've done exactly what you've described and never ran into that problem. Quite the opposite in fact, on some dev servers I've have to manually fudge the auto increment number because it didn't automatically reset to zero after I'd flattened the table.
Like I said before, you can even create an empty table and define the auto increment to be 10000 if you wanted. So there is a persistent value that's stored. However I suspect the issue here is that I'm using a different MySQL engine to yourself.
Like I said before, you can even create an empty table and define the auto increment to be 10000 if you wanted. So there is a persistent value that's stored. However I suspect the issue here is that I'm using a different MySQL engine to yourself.