Hi Marcus,
Which board exactly are you using, is this an R series PCI board?
I was not able to find any known bug with LabVIEW 8.0 FPGA module relating to hanging PWM outputs. Have you been successul in generating a single PWM signal, or what happens there?
One thing I recommend is to work from one of the shipping examples for the FPGA module that does PWM. From Help->Find Examples, do a search for PWM and you will find an example such as PWM Out, Simple.vi . This way, you're ensured that the code is fine. Then, you could add in functionality for the second one with (potentially) different duty cycle.
Let me know how that goes for you, Marcus.
-Sam F, DAQ Marketing Manager