Are you dealing with a Nation Wide Bank (such as a Chase or Bank of America) (I am assuming not if the branch is doing it's own scanning) You could request to talk to the President of the branch and go from there. All banks are federally regulated by the FCC.
Credit Unions are not federally regulated. Once again you would probably need to speak to a branch president and if that doesn't work then ask to speak to the regional president.
If you are referring to a BANK holding cash for 3-5 days that is against FCC . I have dealt with a LOT of banks and even worked for a few and I have NEVER encountered a bank (or a credit union) that puts a hold on cash. I think that you are misunderstanding their policies. Also if you are dealing with a BANK then the fist $100 of ever deposit (this would be checks as cash is always immediately available) is always immediately available (this may actually be the first $100 of any check rather than total deposit).
As far as your check being returned. If they pulled then money out of your account then it should be being handled like a returned check. Your bank should be able to provide you with the "returned" check and then you can go to your customer and ask them to replace the check.
As far as your branch tellers scanning their own checks...they should be balancing EVERY batch that they run to verify that everything has been caught and scanned. If they are not balancing their batches then I would definitely talk to the president as this is very poor policy as a whole.
Good luck. Definitely sounds like you are working with a small community bank or credit union.