So it's the latter: means that the master public key may be intact but the master private key doesn't match the addresses in the wallet file.
In cases like this restoring the seed phrase is the usual solution,
but since it only restores the old transactions, I'm thinking that the newly generated addresses which are the funded ones are somewhat unrelated to your wallet.

However, upon checking the master public key, it appears that there are funded addresses sneaked into the wallet file which aren't related to the master key.

The interesting part is, if you enable "LabelSync" plug-in (Tools->Plugins->LabelSync (restart)) there'll be lots of notes in each transactions containing private keys and "I am satoshi" and "JeffreyLee" notes.
You're satoshi, right?
No seriously, I find it difficult for a regular user to add his addresses' private keys as transaction labels.