Actually it is not so strange, here is why. With your normal mini display port to HDMI adaptor you are plugging into the output of the video card. Even though the port is also a thunderbolt port, the HDMI adapter is not a thunderbolt device. The video card is 100% designed to get information from its memory process it and display it.
The blackmagic output is not a video card and is a thunderbolt device (or usb3) (essentially a PCIe card attached by a cable).
VIdeo cards are optimised for processing and displaying video, these new GPU actors take full advantage of that. The process that is happening (lets say you are playing a movie) is: the movie is read from the disk, if it is in a codec that is hardware accelerated for decoding, the data should go from the disk and get uploaded to the GFX card and then decoded (the uploading is slow), then the GPU actors do their magic and the data does not leave the video card. Without a blackmagic outpt, from a normal HDMI the video can now be displayed (pretty much)
When you then want to output the image on the blackmagic device it has to push the image to a pixel format and send it through the CPU and ram to the PCIe bus where it is caught by the blackmagic subsystem and then pushed out as pixels (if this is via a USB 3 device there is an extra step of filling the buffer in the USB 3 controller.
The extra steps to get back to blackmagic from the GPU are all slow and costly operations. Depending on your computer and what else it is doing you may have just run out of resources. Also depending on your hardware some USB 3 controllers are really slow and although the full spec will support HD video, many manufacturers cut corners and you end up with a slow and crippled controller.
You may be able to get better results by optimising the system- what video codec are you using, is it GPU optimised? How much ram do you have?
