@loki So, I'm not at the "knows all the command-line switches" stage; I've worked with it as part of building a live transcoder for work but we only do streaming, so I've never tried to use it as a splicer.
That said, maybe you could do the trimming in stages? If you can reliably cut the first 5:10, do that on the first pass, save that to a new file, then come back and trim everything after on a second cut?