I normally delete the contents of Market_Saved & Market_Prices and it sorts itself out after that
they will re-appear if you continue adding and removing items and as for the lag, could it not be caused by the mobs spawning when you reboot? Depending on how many have to spawn can make it a lil laggy for a while so get the items sorted that you are adding/removing then give the server some time to get respawns outta the way and see if it still lags
