The current reporting feature simply uses the system field name for the Y axis. In some cases this causes it to display an incorrect axis title. For example, if I create a report to chart the average duration of an issue, the field I would need to use is Planned Duration in Minutes. The aggregate of this field is automatically displayed as days, yet the Y axis uses the field name and displays minutes. Obviously this is not only confusing, but completely wrong. The values being displayed are simply not in the correct unit of measure.
The simple fix for this would be to have the chart obey custom field names entered in either advanced or text mode.
Attached is a screen shot example of this in action. I am submitting this as a product improvement request, but I think this might just as easily be called a bug.