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After reading your post I checked the box of my 520-series SSD (purchased new from Amazon over a year ago) and observed the serial number matched the orange seal label and what's printed on the outer box label. But the serial number that appears when running the Intel SSD Toolbox is a completely different number.
Don't worry about it. I'm sure your drive is fine
I agree with Brad.
If Intel is like most manufacturers of consumer electronics they don't test every unit produced, but pull samples either at random or at specified intervals (there's a lot of argument over which practice is best) and validate the "pulls" against manufacturing and performance specifications. This can take place at the factory and/or somewhere else in the distribution chain. Some companies recycle pulls after testing, some return passed units to the retail chain. I don't know what Intel does.
I do know that Intel has (or at least had) a policy against selling returned, but functional products (aka refurbished), as new stock. Your retailer may have a different policy, but as long as the sticker on the anti-stat bag was intact I would not worry about it.
Retailers may crack the box seal to verify the box actually contains a product (or the right product) before making it available to customers. The problem of thieves (and employees) intercepting shipments, opening the boxes and substituting worthless items is becoming more widespread. There was a story going around the Internet just this week of a guy who ordered a laptop from a popular manufacturer and found the legitimate product box contained hardwood flooring scrap. As did the replacement. And the replacement's replacement.
In any case, your 520 series has a full five year warranty so if you're concerned about it make sure you keep the paperwork handy and verify that your backup strategy is as robust as you hope it is.