Lori,
sounded like you only backwash only once. I would suggest to repeat the backwash procedures minimum 3 times before set it to filtering again.
I think the filter takes about 3 to 4 weeks to build the biofilm bacteria so after 6 weeks in operation, it should be functioning as designed.
for dirty water, it depends on feeding or whether you have settling tank in from of the filter or not. if you feed alot, then the water will get more dirty. on my filter, dirty water come out in first 20 to 30 seconds and then clear water come out. I normally perform the backwash procedures 6 times once a week.
Steve