Most likely the "first" $500 is the fine for having built a pier without a permit. The others are the annual fees that would have been paid over the time the pier was in place, had you been issued a permit when it was built.
DNR is still in charge of pier permits, collecting fees and deciding what the fees will be. DNR does not want to hand this portfolio over the SPTB. SPTB would like to have it, but cannot take it over unilaterally.