I've been here with the same issues as you describe however I am not in a position where I can view your video (at work) the big cause I had with my motors stuttering/jamming and making huge bang noises when moving was that the parallel connection with the PC just could not cope with the signal so was missing steps left right and centre, although an expensive move from myself I brought the UC400 Ethernet adapter and it fixed the issue; other alternatives are the UC100 USB plugin (cheapest option) and UC300 Ethernet.
However Jazzcnc is very good and helped me as well as others have/are so peace of mind you will find out the issue/s in time and get it working.
Also the USB plug in that came with my 6040 was a fake and I binned it, the software with it was horrible and Mach3 was pirated, I downloaded the trial version from New fangled solutions web page and started a fresh by deleting what I had from the seller.
By no means would I say that you should feel foolish with getting the 6040, it will be a learning curve but I'm taking it the positive way now as if it worked from the get go I would probably be none the wiser on how the machine works, how to maintain it what to look out for if any issues etc. and most likely brake it through ignorance of being a plug and play customer with dodgy software/components within a year.
I hope this helps.
Graham