I'm also seeing the same problem, just with heartrate though.
I've started doing a few workouts on my rollers recently using just a cadence sensor and my HRM, and recording the session using Maximum Trainer and noticed the heart rate doesn't flash during these workouts. Which would indicate it might have something to do with the power recording that is causing the blinking. I see that the source code is now on Github, I might have a look at it when I get sometime and see if I can see what may be causing the issue.
(its not really an issue though, the heartrate date is still recorded perfectly)
Installed Maximum Trainer and I must say im impressed with it. It works perfectly with my Stac Halcyon.
The FTP test is confusing. It states to follow the green bars, which offcoarse is false. It would be better to mention that you have to cycle the 20min test part at the max you can sustain. So dont follow the green area for that part.