The timeout mechanism in ser-unix.c was changed in commit 048094acc.

In do_hardwire_readchar(), the required timeout is broken into 1
second intervals and wait_for() is called.  Before, wait_for() set
VTIME and VMIN so the read would block, but now it uses select() to
block for the specified timeout.  If wait_for() returns
SERIAL_TIMEOUT, do_hardwire_readchar() returns immediately, so the
timeout is always only 1s.

The attached patch will repeatedly call wait_for() until the full
timeout has elapsed.

Gareth