Units have good and bad clerks, but not everything that goes FUBAR administratively is the fault of a clerk. For example, OTs, Component Transfers, promotions, etc will all pass through the hands of your CO, OC, Adjt, RSM, CSM as need be. Many is the time that I have typed up all the relevant paperwork for a promotion or some such, passed it in to the chain of comd and it has mysteriously disappeared. Usually, after the OR staff have taken the blame and the soldier is pissed at his OR staff, I will have a mildly confused staff officer walk in to the OR wondering why he has this paperwork on Cpl Bloggins that is dated from a few weeks ago. The officer that has that paperwork in his hands now, was denying a few weeks ago that he had ever even seen it.
Clerks aren't perfect, but they don't cause all the administrative problems in the CF. Sometimes it is the clerk's fault, other times a staff officer is to blame and sometimes the soldier in question has caused his own problems.
But, if you aren't receiving the level of service you believe is acceptable, definitely advise your chain of command. If the OR staff is up to snuff, you will receive a reasonable explanation of what is going on. The soldiers of a unit and the chain of command that the clerks are there to support. If they aren't doing that, you deserve to know why.
Best of luck. Cheers.