just so i’m reading this correctly.
You left the keys on the original graphics, so they were essentially keying over black (providing the fill on your video output)
You then put a pass of the matte only (dove into the key and pulled the matte out, placing it on the timeline?)
When you output, the keys on black worked, but the output file ignored the mattes only portion.
I can’t think of any reason this would happen, except the obvious…you had an incorrect in/out set on your timeline.
When i do clean keys at the end of the program, i would usually go fill then matte, then fill, then matte, so its easier to find the cooresponding matte for each key. Try this and see what kind of an output you get.
You could also put a flash of bars at the very end and see what kind of output you get.
Glenn