I cannot see the 1st screenshot in the topmost post.
If the number of faces / vertices / poistions mismatches, then OpneBRF will refuse attempting to merge them into a animation.
If the problem is that the frames are garbled up, then the problem is the internal vertex ordering. It is difficult to solve. One sure way is to edit your vertex animation entirely in an external application, then export it as MD3 and import it in OpenBRF.
Else, a way out is try making sure that, in all frames, different vertices use different texture coordiantes (no matter how close, as long as they are not the exact same number), so that OpenBRF can tell which vertex of the (say) 1st frame is which vertex of the (say) 2nd frame, then make sure you set [Settings]=>[On assemble vertex animation]=>[Trust teture positions to be the same], then assemble the animation one frame at a time, copying a frame at a time and pasting it as a frame (Ctrl+Shift+C) into the animation.