There is a fundamental flaw in how you calculate cycle time in develop. It calculated from the 1st in progress step on the workflow. If you rigidly follow each step then it would work fine, but in Kanban you can skip steps if they don't apply. Your current approach excludes any item that does not have a date on the 1st column. So for any items that skip step 1 they are not in the chart, they have an effect on the cycle time calculations and you are ignoring them.