Don't look at total fee amount and amount being sent... They have no real impact on the priority of your transaction. Priority is generally a factor of the "data size" of the transaction. So, you need to look at the fee "rate"... usually measured in satoshis per byte or BTC/kB.
The resource in demand in bitcoin transactions is block space as that is the limiting factor... so, due to the supply/demand nature, the larger the space you want, the more you have to pay. that is to say, Miners prioritise transactions based on how much they're paying per byte of block space they use.
ie. if your transaction is only 226 bytes, you don't need to pay as much (in total) as someone with a transaction that is 2260 bytes... but you'd want to pay the same rate!
You can see recommended fee rates here:
https://bitcoinfees.earn.com/ and here:
https://btc.com/stats/unconfirmed-txThe differences in the fee estimation may genuinely be a bug... but it is likely that the wallet is just using different "coins"... perhaps try enabling coin control features (Settings -> Options -> Wallet) and see which coins are being selected when you're attempting to create the transaction.
HD Key Generation should not have any affect on the transaction sizes/creation etc... to upgrade, you'd need to create a completely new wallet... and transfer your coins from your existing wallet to the new one.