I think I figured out how to make it work, but I don't really understand why.

If I move the code I was running using -e on the command line into an eval_pv, then just eval "1" on the command line, and do all my eval_pv's before calling perl_run, things seem to work.

E.g.:

interpreter = perl_alloc( );
perl_construct(interpreter);
perl_parse(interpreter, xs_init, argc, argv, NULL);
eval_pv(install_sig_handlers, 0);
eval_pv(my_code, 0); // profiling, debugging etc. work
perl_run(interpreter);
perl_destruct(interpreter);
perl_free(interpreter);
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