It's actually a good question. Let's take a look at what is happening. First, Electrum hashes your mnemonic to generate a seed. The seed indeed contains all the information necessary to generate the Master Public Key and the Master Secret Key, first being used to generate the sequence of public keys (adresses) and the second being used to derive a secret key from a public key (actually it's slightly more complex). Then, Electrum saves the wallet file, which contains the seed and the keys being actually in use, the whole sequence of key pairs unless it hits 5 consecutive unused adresses. It can store it either unenrypted or encrypted. In the first case, the seed value in the file will always look the same, as will private keys. In the second case, however, they won't. Why? The Electrum documentation says:
Electrum uses AES-256-CBC to encrypt the seed and private keys in the wallet.
What does it mean? AES-256 is simply a block cipher. It takes a block of data (128 bit in this case) and a block of key (256 bit) and outputs 128 bits of encrypted data. But it is not what Electrum does. Actually, noone uses block ciphers like that and noone ever should. Instead, so called modes are used. In our case it is Cipher Block Chaining (CBC) mode. Electrum first generates a random initialization vector (IV), mix it (by exclusive or operation) with first 128 bit of input and uses AES-256 on this mixed block to produce first encrypted block. For any subseqent block it does the same, except instead of IV it takes previous encrypted block to mix with the plaintext block. The IV is saved alongside with the file. Finally, that's why you always arrive with a different seed value in a file, even when using the same password (which results in the same key for AES-256-CBC encryption ) -- a different IV is used each time.
 It is not probably the case either, as Key Derivation Function is likely to be used to deliver a key from your passphrase, in which case additional random salt value is added to the passphrase before hashing it and saved alongside, similarly to the IV.