Atomos Ninja Star won't capture from Jitter or Isadora

I just purchased an ATOMOS NINJA STAR with hopes of capturing/documenting my video generated with Isadora and Jitter.

I am running Isadora and Jitter on a 3.06 GHz Intel Core i3 with 8gb ram. The Ninja Star takes a micro hdmi input, so I go from Thunderbolt-to-HDMI-to-microHDMI via an adapter.

At best, I can capture 20 second clips before the Ninja Star loses it's "lock" on the video stream. A tech support representative from Atomos told me that The Ninja Star (as well as other Atomos products) require a certain quality or consistency of video signal in order to capture properly. Isadora and Jitter do not output a signal that meets these requirements. The Atomos representative wasn't well-versed in Isadora or max/msp/jitter, so I figured I'd put this up here and see what people have to say.

A couple interesting points/concerns:

1- The tech support representative said that ALL Atomos products essentially function in the same way. Has anyone successfully captured video from Isadora with a different Atomos product such as the Ninja Blade or Ninja 2?

2- The Ninja Star has no problem capturing my display in other instances. As I type this, I can record my display fine.

3- The Ninja Star did not properly capture from Jitter or Isadora, but failed with each in DIFFERENT ways. With Isadora, I would capture a maximum of 20 second clips. I noticed the "lock" would fail almost immediately after I full screen my video stage. The video on my display would not be affected. With Jitter, the Ninja Star negatively affects the quality and behavior of the imagery I am generating. The clips I capture will also be broken into chunks of generally 20 seconds or less. The quality of these clips is more varied than those from Isadora.

4- Can anyone recommend a method for capturing live video from Isadora and Jitter that will work, look as good as it does on my display, and not cost me over $1000? The only method I've tried that works is a Blackmagic Hyperdeck Shuttle with a DVI extender and an SSD. That's more $$$ than I can spring for.

Thank you in advance to anyone who may offer any insight into this. (I also posted this on the Troika forum)