The Vault only reads the exact Cardano address you verified with it, it doesn’t scan every address in your wallet. Even though your wallet app shows a combined balance, the Vault will only pick up WMTx held at that one on-chain address.
If you’ve received tokens across multiple addresses, just send them all into the address you linked to your Vault. Once they’re consolidated there, the Vault will see the full amount and stake it correctly. Otherwise any WMTx left on other addresses might not show up until you move them over.