The workaround is to create your flow chart in PowerPoint, copy and paste it into Keynote. It will then work like any graphic element.
Otherwise, create your flow chart boxes, place them in their positions, then use the line tool to create the connectors. Use the copy and paste function so you don't have to create each individual connector.
Keynote allows you to center and register your graphic element (in this case, connectors) quickly and visually with guidelines that automatically appear to indicate its position in relation to another graphic element.
Please check out my example at "http://dogzenart.com/keynote/InventoryFlow.html"