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Do both accounts have the same xpub and derivation path (in the account details)?
If not, that means that they are different accounts.
That could be because your seed is in fact different, or because use use a bip39 passphrase, or, more likely, that you created a different BTC account, for example an account of a different type, or an account with a different derivation path.
If both accounts have the same derivation path and different xpub, it means that each account was created from a different seed.
If both accounts have different derivation paths (and xpub), it means that they are different accounts, so it is normal that they don’t have the same balance.
Note: It is technically impossible to have different derivation paths and same xpub.