O Oh , trust me this could turn into a bigger cluster &^%$ really easy. May I ask a few questions first? Was the shipper (the person you got the trans from) versed in shipping things via common carrier? Correct labeling and palletising? We ship common carrier often, and to the inexperienced shipper.... well lets just say it's not like throwing something in a box and running to the post office. (Of which i also have stories on.) Lets start with a good pallet, it dosen't have to be good looking but sturdy is a must. Also having the frieght well affixed to the pallet is very important. We use cattle wire that we twist to take up the slack, some people use banding, I have found this to be very ineffectinve on oddly shaped frieght (like tranny's). Proper labeling (SMUDGE PROOF) is another factor.
I'm on a roll now so bear with the story. Joes sells a trans. Hes never shipped anything before. He ties it to a pallet and puts your address on a piece of paper and tapes it to the tranny. Mike the fright driver goes to Joe for pickup. Mike puts the bar-code sticker on the paper next to tour address. So the terminals can scan it. (I belive just about all frieght companies are using this method by now.Now it goes in the truck to the terminal (not directly to you) . BTW a piece of frieght could go through 10 terminals depending on where you are and if the frieght is going multi-line. ( Which means one carrier picks it up- another drops it off). Still awake?good! Now the frieght is on the road, belive it or not pallets do "bounce" at times in the back of trailers. Now the piece that wasn't properly affixed is still on the pallet, but already loose. Which is also playing havoc on the pallet which was not that study when Joe pulled it from the dumpster. Mike gets to the teminal , its raining as his trailers unloaded. The address paper gets a little wet but it still there. Now the pallet gets moved around a bit in the terminal. Part of the banding holding the frieght is very loose. It goes in the next truck and gets bounced around a little more. Frieght gets moved around , the paper with the bar code gets torn off. By the time the pallet is unloaded again. the frieght is totally loose and comes off the pallet altogether. The labels gone...the pallets junk... the frieght lays around in he terminal. FAST FORWARD here... Bill calls the trucking company after waiting for his frieght for weeks .. the las record they have is when it was scanned at the first termial. And trust me Mark who works in the office is NOT going into the terminal to physically look for Bills frieght. And on and on and on. Although this is a fictional story, we have had a piece go missing for 7 weekls once. And companies both common carrier and of the FED-EX variety all work this way. The other bad part is it's just another thing to move for them. Unless you insured the trans most frieght companies only have a $50 liability on used mechandise.
If it comes down to it, and if you paid with a credit card (Visa, etc.), just contact your credit card company and explain what happened. They will credit your account and relieve you of the hassle. This is why I ALWAYS use my credit card for big and/or potentially complicated transactions, e.g., eBay. 
This is very good advice. Best of luck!
