We have this problem frequently as we operate at the public index terminals.  Our clients frequently hire couriers to bring documents to us here.  They are oft mis-delivered to the county and end up in a mail room,  then routed to the Recorder (Registrar of Deeds).

The Recorders staff usually do not receive them with fee payment included and hence reject them, returning them to the addressee.

However, on occassion, such things are sent with blank checks as payment. 

Firstly, I do the same as you;  I'm not going to run the names on a package that was never delivered to me for the datedown liability.  My clients are responsible for ensuring that the documents reach me and must be able to track deliveries (which is why they pay couriers to do so).  If my signature does not appear on the receipt, then it didn't arrive to me and I will not  knock on 50 county agency doors to see if it's on one of their employees desks. 

Secondly, I have a systematic process that I engage in whenever something is "missing".  I tear apart every paper, one by one.  I direct the client to send me copies of the papers, copies of the shipping tag, copies of any voucher / cover sheets and copies of the tracking data.  I cross-check all this data to ensure that the file references are consistent (not mislabelled), names match, the property is within our jurisdiction, the land descriptors are all within our county, etc... 

Finally, I remember, with any client to include wihtin our contracts a proviso that puts the delivery tracking burden on the client and that absolves us of any liability for documents that are not in our possession (this includes when they get submitted by us to the Recorders Office staff, or if they never arrive to us in the first place, or if they are returned to the client upon client-request).