it could be carp pox but i'm not 100% sure. if you could tell me more about the set up you have then that may point the finger to what your fish may have.
how many gallons and how many fish are in the tank?
any new additions before the marks appeared?
what is the temperature of the tank?
you have said you do a water change every couple of weeks. this may not be enough to keep the water clean.
have you any test kits for ammonia, nitrite, nitrate and ph?
if not then you can get some water tested at your lfs and ask them to write the results down.
when you do water changes do you do a gravel vac as well. this is really important for your fish.
the filter needs to turn over the water 10 times every hour for it to be effective.
the good news is that if it is carp pox then it will clear up with good tank maintenance and more regular cleaning of the tank.
you have also said that you change the media in the filter each month. is this the sponge that you are throwing away? i am not from the u.s so i am unfamiliar with the filter you have. if you are throwing away the sponge then you are getting rid of all the good bugs in the filter which eat up ammonia and nitrite. sponges should be rinsed each week in used tank water and then replaced back in the filter.

thats a lot of questions i have asked and i apologise if you already are aware of most of it but i like to get the whole picture where possible.
in the meantime do a 50% water change twice a week and use a gravel vac at the same time. dechlorinate all water going back in and i hope the pox (if that is what it is) will clear up. and please try to get those water tests done. thank you and hope to hear from you soon.