Your filter and gravel are the media where food for good bacteria is stored (krud) If you clean the filter and the gravel you remove the food and the bacteria die off,or are removed with the krud. The tank cycles by establishing a balance between bacteria and food so that the nitrogen in the fish waste (urea) can be converted to ammonia then nitrite and nitrate. The plants remove the nitrate. Think of the filter and gravel as a living thing and allow it to become host to all the good bugs that will establish the balance in the tank, rather than trying to keep the tank clean/clean.