Hello,
I downloaded a build of the PWM eTPU function from the ASH WARE eTPU Code Builder and then got it up and running in simulation using your configuration - MPC563xM, 80MHz system, TCR1 at 10MHz. All looks fine running 0 to 100% duty cycle. I also downloaded a build from the CodeWarrior eTPU Function Selector and as expected that works the same.
This code:
/* initialize eTPU */
if (my_system_etpu_init())
return 1;
/* start eTPU */
my_system_etpu_start();
/* initialize a PWM output at 20 % duty, 20kHz */
fs_etpu_pwm_init(ETPU_PWM_CHAN, FS_ETPU_PRIORITY_HIGH, 20000, 2000, FS_ETPU_PWM_ACTIVEHIGH, FS_ETPU_TCR1, etpu_a_tcr1_freq);
at_time(1000);
fs_etpu_pwm_duty(ETPU_PWM_CHAN, 10000); /* 100 % , 20 kHz */
at_time(2000);
fs_etpu_pwm_duty(ETPU_PWM_CHAN, 0); /* 0 % , 20 kHz */
at_time(3000);
fs_etpu_pwm_update(ETPU_PWM_CHAN, 10000, 10000, etpu_a_tcr1_freq); /* 100 % , 10 kHz */
at_time(4000);
fs_etpu_pwm_update(ETPU_PWM_CHAN, 10000, 0, etpu_a_tcr1_freq); /* 0 % , 10 kHz */
at_time(5000);
fs_etpu_pwm_update(ETPU_PWM_CHAN, 10000, 5000, etpu_a_tcr1_freq); /* 50 % , 10 kHz */
Produces this output:

I've attached my project for you to look over - you should be able to use the etpu_gct.[c,h] files and other pertinent source to try it in your setup, or at least check out code differences.
John Diener