Same 'problem' here. On a 10GB partition with 1.9GB free there's a message that less than 5% is available. This is in both the latest 1.x version as in the BETA.
Please have a look at this. It seems a bug because it does defrag.
When calculating the amount of free space before defrag, Defraggler takes into consideration only the free space which is outside the MFT zone. We would not like to see any files moved into it, as it is the free space reserved by the system for future growth of MFT. It is allocated only if the remaining space (outside the MFT) is used.
As you can observe on the screenshot attached to the first post, the MFT zone may be pretty large.