Maybe you’re creating contours of a set of stairs?
Did you try to split the SRTM2OSM output before passing it to mkgmap? If it’s sufficiently small to not need to be split, you may be able to open the OSM file in JOSM and see whether it’s OK (in which case the problem will be with mkgmap).
If you’re only making a contour map, and have no other data to process, then you don’t need most of the mkgmap options you’ve used though I doubt that’s the cause of the problem.
I have no idea if the order of the command-line switches for SRtm2osm matters, but for what it’s worth, I have no problem when running commands of the form:
I found that I had used the wrong hgt files from http://viewfinderpanoramas.org. I think I used the 1" instead of the 3" versions. With the correct files, it works beautifully.
Thanks for your helpful responses. The suggestion of checking the osm file with josm helped narrow it down.