According to the manual, each "PWM cycle" takes about 5ms with a 4Mhz clock. My guess is the first example has the interupt routine taking longer than the time between interupts. And you are prolly getting lucky to ever leave the handler at all!

The second example using pulseout, looks much better. Hard to count the lines, is it the correct timing?

Now remember, you don't want the pulseout in the interupt handler.