If I add a folder to my favourites and then I click on that folder, my folder tree will jump all the way to wherever that folder is on my desktop and then I need to scroll all the way back up to get to my favourties again.
Do you mean when you go into a sub-folder below the favorite, not the favorite itself?
I think so. Basically when I click on a folder that is a favourite or navigate below that folder.
Clicking the favorite itself shouldn't scroll the tree.
Going into a folder below the favorite will, since there's no other way to show the folder you are now in.
(Unless you configure the tree to not follow your current location, similar to how the tree in File Explorer works now. But if you only use the tree as a list of favorites like that, then putting the favorites on a toolbar probably makes more sense, if you don't want to access them via a menu.)
Apologies, you are correct, it is only for subfolders. Glad to hear I can disable that 
Where is that setting?
Also I am using the favourites on my toolbar as well, however, I like having the folder tree as well.
It looks like disabling "Automatically expand to current folder" in "Expand/Collapse" under "Folder Tree" in Preferences has somewhat helped, however, it still moves the focus from my Favourites to the disk on which the folder is stored.
Is it possible to change that?
Turn on Preferences / Folder Tree / Appearance / Show lock button, then click the lock at the top of the tree.
Use Settings > Set Lister Defaults to save the lock state for new windows.
(Alternatively, turn off the Folder Tree entirely, and use a toolbar/menu to list the favorites.)
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Awesome, cheers. Is it possible to hide or otherwise customise the new header?
Preferences / Folder Tree / Appearance / Show Folder Tree header
Unfortunately, the lock button is dependant on the header:
Make a hotkey or toolbar button with...
Set TREELOCK=toggle
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