I had the same problem on 21 January 2019 I receive a replacement for my Ledger Nano S due the firmware upgrade, after the initial setup I move 1.9678 BTC to my Ledger than I have stored the key on safe place, a few weeks later I connect my Ledger in order to move some coins and I discovered than my balance was 0.
I checked the transaction and I find that on 29 January 2019 that someone has move all my BTC to this address:
36bbmZdw73MCN93qWE69X4pcJ3AS6dH3Rj
this is the TX ID: 8629187cb30f4e1facf5ba03f7426b19f2270aa4a48e299e10ff3b851d7de7ea
I never been able to have back my BTC
Probably your ledger nano was not genuine, hackers and scammers have been selling a modified version, beware.