Uploading a new custom icon in plugin configure screen does not actually save icon in themes or plugin folders. Additionally, a custom_icon.png is ignored. Perhaps this is a Windows/Bitnami stack specific rights issue with the Apache server...
My workaround was to manually copy in my company icon. File custom_icon.png did not work - I had to delete the fedmine supplied icon.png file and name my icon file icon.png. That worked (cleared browser cache, too).
Great looking theme!