How have you added new accounts to your MM? Once you are using a hardware wallet you do so by ONLY going through the "connect hardware wallet" steps and choosing more addresses from the list of addresses. Remembering to make sure to change it to BIP44 if it was originally a MetaMask seed.

If you clicked "create account" within MetaMask, then any address created tghis way is a part of the seed which was used to set up MetaMask. If you followed my guides and setup a "DUMMY" MetaMassk, then these new addresses are a part of the DUMMY seed and have nothing to do with the one on the Ledger. Hope that is not the case....