Wait, you are supposed to check in to customs?  In the town of Ely?  So let me get this straight, you can paddle across, stash whatever you were smuggling in the woods, then check in with customs, and then go pick up whatever it is you were smuggling? 

Sounds like more of a hassle for regular people than anything else.  The whole notion that someone with something to hide is actually going to check in with whatever they are hiding in the hopes the customs agent doesn't find it is absolutely absurd.  They are better off doing random checks at Prairie Portage or something.  More annoying, yes, but at least it would be effective.

We checked in at customs in Ely on our way back yesterday.  Showed our passports and THEN had to fill out a pieces of paper with name, address, etc., etc.  which we thought was redundant paperwork since the attendant also scanned the passports.  The officer took a cursory look in our car...didn't see much, it was so stuffed there was only minimal room for us three passengers to squeeze in. 
I often have not checked in on past trips but have never heard from them that they missed me.  Once I checked in and they were not there, so I stuck my Canada permit copy to the door and left a note "I was here".
Once my dad did a Quetico "walk" and after he got back they called to see if he ever showed back up at home.  Again, no repercussions 

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You're lucky that you weren't fined for importing foreign soil without a permit.

Paddlemaker and I also had our vehicle "searched" upon our return to the U.S. on Saturday morning in Ely. We speculated that the officer on duty just liked the smell of funky old paddling clothes and camping gear after several days in the woods. There is no other reasonable explanation for a search in a situation like this.

On this trip to WCPP, I passed through the U.S. Customs entry/exit to Canada at Pembia North Dakota (on I-29 south of Winnipeg).  On the way in, it was smooth sailing (of course) and took less than 10 minutes (and a few questions) to be on my way.

On the return, on Thursday, I had the nearest thing to a strip search I've yet encountered.  Of course, with the extra screening it took maybe 25-30 minutes of waiting in line to reach the first screening point.  I answered the typical questions and was then directed to "Bay 2" for further inspection.  I waited another 10 minutes for the bay to clear of the previous occupant (this was like a drive through garage with doors at both ends).  Once I was directed to pull into the bay, I was asked to step out, face the stainless steel table and empty the contents of my pockets onto the table and turn my pockets out.  After an expection of the contents of my pockets with additional questions, I was escorted to a waiting room with "one way" glass.  I waited approximately 20 more minutes until I was excorted back to my vehicle and was permitted to continue on my journey.

I can only summize that the staff needed something to do.  As I pulled into the bay, my vehicle was surrounded by 8-10 customs agents!    There looked to be 6-8  such bays, but I couldn't tell if all were in operation ... but any way you cut it, that's a lot of people!  Commercial traffic had its own, independent, screening facility.

The good news was that the agents were friendly and courteous and the surroundings were very nice and clean.

dd