5.5.3>5.5.4 requires reenter of passphrase even though saved

I use WinSCP Portable which means to update I download the new version and then replace the 'data' folder with that of my old version so that all my site definitions are imported. This process of using the portable version and updating in this way has worked well without issue for a long time now. However, updating from 5.5.3 to 5.5.4 I noticed that for sites where I am using a private key, even though my passphrase is saved with the site definition, 5.5.4 keeps asking for my passphrase every time I open a new connection.

See attached demo.

Here my connection has the correct passphrase saved already. I double-click to open the connection and WinSCP 5.5.4 prompts me to re-enter the same passphrase already saved against the site definition. I then paste in the same passphrase in the prompt and my connection is opened successfully. Not sure why it's prompting as falling back to v5.5.3 everything works as it should.

Are you talking about a private key passphrase or a password. The passphrase cannot be saved.

Please attach a full log file showing the problem (using the latest version of WinSCP).

Yes, I am talking about a passphrase.

In 5.5.3 you can save a passphrase - I can make another demo GIF demonstrating the same saved connection (as used in my previous GIF for 5.5.4) but this time I am not prompted to enter my passphrase as it is already saved.

Logs attached for both 5.5.3 and 5.5.4

OK, you are right. But that's was an unintended behavior in 5.5 – 5.5.3.
Actually this bug:
Issue 1176 – When remembering session password is enabled, stored password is used twice, even for two distinct consecutive keyboard-interactive prompts
Though its wording does not cover your scenario that I was not aware of until now.

How do I therefore save my passphrase with my connection details so I am not prompted every time I connect using a private key?

Please read documentation:
How can I connect without entering private key passphrase each time?