Aha! relies on time tracking in JIRA being set to the default value of minutes. If the value in JIRA has been altered to anything else, it throws time tracking estimates off.
As of the 6.4.x version of the JIRA REST API a GET is available that returns information on optional JIRA features including the full configuration details of time tracking.
Aha! should utilize this to detect the default value and adjust estimates according to what the JIRA instance has configured as the time tracking value.