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Most likely, the script you use does not follow the BIP39 standard. BIP39 standard means adding mnemonic word as a salt and concatenate it with the seed. After that the whole seed together with added word "mnemonic" is hashed 2048 times with HMAC-SHA512 and you receive the 512 bit number consisted from master private key and chain code (256bit each) as left and right sides).
So, you should be sure that the script you use follows the BIP39 standards. It seems it is not. For example, for BIP32 standard you need to use HMAC-SHA512 with the key Bitcoin seed.
Have a read this topic, probably it will help you as well: https://bitcoin.stackexchange.com/questions/84116/get-master-private-key-from-bip39-seed