ReCalcitrant Court Clerks

We had a brief due at noon. The paralegal filing the papers called me a few minutes after, and told me that a clerk at the SDNY refused to accept the papers, because our expert's declaration bore a faxed signature. I had him file the rest of the papers, albeit a few minutes late, rather than take their bullshit Hobson's choice of seeking out a magistrate to determine whether they should take all the papers. Bastards.

Upon his return, the paralegal could not find a rule prohibiting faxed copies, so he called the clerk's office and was told that this is their customary practice, and they couldn't cite a rule. After re-reading the entire local rules, and the judge's rules, and after we found them notably devoid of any rules whatsoever on this subject, the senior associate DA got all pissed off and pointed out FRCP 5(e), which states, in pertinent part:

The clerk shall not refuse to accept for filing any paper presented for that purpose solely because it is not presented in proper form as required by these rules or by any local rules or practices.

(Emphasis added). Even if the SDNY or the Court made a rule, the FRCP prohibits rejection. Furthermore, local and court rules can't trump the FRCP.

Unless opposing counsel makes an issue of it, no harm no foul. But what I really wonder is, do we have any recourse for the clerk's improper behavior, clearly in violation of the rules? Further, should we clear up what is apparently a widely held belief in the Clerk's Office that they can willy-nilly reject papers on whatever basis they wish, despite whether it prejudices the litigant, our client?