Freqtube is a real-time hardware based plugin and real-time rendering needs to be used in your DAW project when bouncing or recording (not off-line bounce).
The freqport system runs separately to the main audio I/O used in your DAW. Use a Core Audio or ASIO driver as your DAW main audio interface and ensure your project plays in real-time without audio dropouts or cpu overloads before using freqtube.
Check the Reason Operation Manual at page 154-159 - Recording audio from Mix Channel outputs
https://a.phcdn.se/Reason12/Manuals/Reason_126_Operation_Manual.pdf
Check the Fl-Studio Operation Manual at Recording External and Internal Audio (section 3)