I find that Voila 3.5 still has an issue when recording on a retina MacBook with dual monitor setup over thunderbolt. The previous version just recorded a green screen selection. Version 3.5 states the file is corrupt on the organizer tab. I have to restart the MacBook with the monitor connected to get this feature to work.
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Could you please provide few screenshot of the issue? Does the feature works after the system restart?
Please do provide us more info of your external monitor. Also do send us your system info and OS details.
Please send the above requested details to our Support Team.
I myself have had this issue (green screen). My only work around is the same as you have provided and I must quit Voila and restart in order for it to record properly. However, I record through the HDMI instead of ThunderBolt.
My system is a Retina 15", 16GB RAM with 10.9 Mavericks on it. I have not experienced the issue since 3.5, but I have only record 2 videos back to back after updating the program.