I have exactly the same problem with Debian Stretch (testing) on amd64. Package version is 232-15.
$ systemctl --version systemd 232+PAM +AUDIT +SELINUX +IMA +APPARMOR +SMACK +SYSVINIT +UTMP +LIBCRYPTSETUP +GCRYPT +GNUTLS +ACL +XZ +LZ4 +SECCOMP +BLKID +ELFUTILS +KMOD +IDN
The system wakes, but the service unit won't be started. If the system wasn't syspended then the timer service works as expected.
