Oh, stupid me.

I can finally reliably reproduce. The issue happens when I try to extend the selection too much, beyond the end of the file by pressing Shift+Down at least one too many times. Or the same thing at the top of the file, trying to extend upwards.

For some reason, my definititon of these macros differs from the one in the default config, which goes something like

rtarw,ltarw,begin_marking,rtarw,toggle_marking  ^[ [ 1 ; 5 C    Mark right Xterm

That right-left (or up-down, etc.) dance at the beginning seems to be exactly the workaround for the problem I'm having.

I'm not sure why a workaround is needed in the config file, rather than it being in the binary, but nevermind.

Feel free to close as invalid.