The addresses may be linked in the future, for example, you receive 1BTC at address A and 1BTC at address B. You need to send Bob 1.5BTC, so your client sends 1BTC from A and 0.5BTC from B in the same transaction. Somebody who is checking the blockchain can see that A and B both belong to the same person.

They are not 'linked' by the same seed.

If you wish to not have two payments link together, you should generate a seperate wallet file and keep the payments in seperate wallets.