Allow me to explain the behavior, and also seek your opinion on possible solutions.

There are two 'working units' in Illustrator. One is at the document level, and the other is at the application level. Former may sound complex, but it is there for a purpose - to enable users work with documents of different units at the same time. e.g., one document with units as Inches, while the other could have Pixels. Control for document's units are in the Document Setup dialog, in the new Properties panel, and context menu (right-click) over visible rulers.

What we see in the Preferences > Units is the application level unit control which applies to all open documents - using which, working units of all open documents could be changed in one go.

There is a third aspect too, closely related to the first one - all documents save their native units. And this includes the document profiles too. What we see in the New Document dialog as Print, Web, Mobile, etc. are .ai documents and hence have a unit saved within. When we create a new document, and start with a document profile, say Print, the new document dialog populates its Unit field (and other fields too) with the default unit of that profile.

What was happening in the last version was that a change in the Preference > Units in a no-document state was causing a change in the new document dialog, turning the profile field as 'Custom', and making it difficult to identify the starting profile. This has changed in the latest update. Now, changes in New Document dialog are preserved and un-related to the changes in Preferences > Units. So, if you change the units in new document dialog and create a new document, this setting would be preserved the next time you bring up this dialog, irrespective of changes made in Preferences > Units.

This was a technical explanation of the two-unit behavior. According to which, the ideal place for making unit changes for new documents is the new document dialog. But it is possible that this may not be the right expectation for users. With an idea to keep the behavior technically correct, yet improve the experience of working with units, we can think of a few simple possible solutions - like graying-out the Units field in Preferences in no-document state, or adding distinct labels like Application Units and Document Units in places. A radical solution could be completely getting rid of this two-unit behavior, which we believe will not go well with users who work with documents of different units. But keeping our thoughts aside, we'll like to hear your suggestions on this. What do you think would be the right experience of working units in Illustrator. We look forward to your ideas on making units work in a predictable manner.

(On a side note, it is possible to create your own Document Profile, which can have your preferred unit, font, swatches, symbols, etc. , and use this profile as the starting point of all your new documents.)

The Units setting in your Preferences will change when you create a New Document with a different setting, it will change to the setting of that document (and that has been like that for ages).

Found a fix. Create a new blank page, change prefs, quit application, when prompted save page to desktop as it closes. Re-open application, check prefs and it worked for me!

Same here, this is so annoying! Also, I cannot set my secondary drive in the scratch disk.
Here's a thought Adobe, use it, fix it and then release it!

Same bug here!

"h" is correct. I tried the same thing and it worked. File>New and in that window change your units to inches and they will remain on any new document you open in the future. Hey Adobe! How about sending some love for the people fixing your mistakes!

I'm having the exact same issue as well since updating to CC2018. I tried two things first that should have worked: (1) changing the units under preferences and (2) right clicking on the ruler and changing it to inches. No luck. Here is what worked, oddly: Start a new document (File>New), in the window that pops up, set the units to inches. Then click create. For some reason that works, it keeps those settings even after closing and reopening.

Preferences not sticking

same problem! so annoying!

Sorry, didn't list the app version: Ai 21.1.0

When I set the preference for Units>General to Inches, it is lost once I quit and reopen. Reverts to points. Tried it with and without a document open. New documents alway open as Units>General>Points. Very annoying.