When you are confused by the output, it's usually a good idea to look  
at what the fields are doing.

e.g. output the fields, or a slice of the fields in the plane of your  
waveguide, every once in a while, e.g. (at-every 10 ....).  That will  
help you understand whether there is some instability, or whether the  
sources/structure are not what you think.

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