Mystery
I think the problem is somewhere near frames buffer. SVPFlow library calculates some frames ahead by avisynth demands. Avisynth store in memory some frames by ffdShow demand. ffdShow store in memory some frames by player (or renderer) demand. Renderer have internal frame buffer to avoid stutter. When seek all these buffers must be cleared and filled again with new frames. I think the clear buffer function of some of these elements from the chain may contain the error.
P.S. I'm not DS-programmer and it is my IMHO.