I understand pixels change between frames due to noise or sync jitter but since the hqx filters work on the linebuffer that cannot be affecting it. The pixels are stable in the linebuffer.
The filters should be working fine even though pixels change every frame. For example a game with scrolling background.
It is a circular linebuffer right? Are you taking into account that when a new pixel comes in all the pixels in the linebuffer shift position? So if you are viewing it as 3 lines then the leftmost pixel on the second line is suddenly the rightmost on the first line.
Does the filter only process the active 256 pixels or all 341?