This happens with all lightsabers that have effects.
Also its not just saber throws that cause it because it happens to my sage with the tythonian saber. She certainly isn't throwing her saber anywhere.
All of this.
I too have reported bugs on this subject. Detailed reports with examples.
Pretty much any ability animation that uses the saber in some way that is not swinging it will break the effect. Throwing the saber, temporarily putting it away to cast something. Even abilities like Guardian Leap revert sabers to default effect.
It feels like the intricate animation implementations involve taking away the saber, using a default/fake saber during the scripted animation, and then returning the saber. The "returning the saber" part does not take saber effects into account. Most likely because it was written before saber effects existed.
PS: If it wasn't clear, this also affects the cartel coin sabers. Feel free to use the Cartel Market sledgehammer to get this bug fixed.