Kanban board cycle time not calculated correctly if issue transitioned in place

When an issue transitions to the same status that it's currently in, the cycle time on the Control Chart report is no longer reported correctly.

This can be duplicated with a new Kanban board set up with the "new project" option and the default simplified workflow and columns:

1. Create an issue, wait 5 minutes
2. Move to Selected for Development, wait 5 minutes
3. Move to In Progress, wait 5 minutes
4. Use the regular JIRA interface or the "more actions" dialog to select the In Progress transition again, so that the issue transitions to the same state.
5. Move the issue to Done

On the Control Chart report, the time spent In Progress is now lost.

The steps above aren't likely to happen, but the same thing happens if you have a custom workflow transition to toggle flags or fields on an issue, or if you are using transitions as a "poor man's field level security" as explained here: https://confluence.atlassian.com/pages/viewpage.action?pageId=149834

Note that after an issue has transitioned through a state once, this problem doesn't seem to occur anymore.

In our particular example, we have a transition on our Testing column to allow testers to update status; when they use this transition we lose all the initial time spent testing on the report. We also have a global, recursive transition to allow limited field editing as described in the link above. Whenever this is used on an active issue for the first time, it essentially erases all the time spent in that column. As both these steps are used frequently in our workflow, this makes the control chart basically useless to us.