Why does Photoshop do this?

It doesn't ALWAYS do it, but most of the time.
And I've never cleared my preferences file, I don't think. If I'm even thinking of the same thing you are.

Hmm...that does actually sound like a preferences file issue.

For a quick reference, every time you open and close photoshop it saves an XML file dedicated to your specific preferences. You'll notice that when photoshop opens up everything is in the same position as it was when you last saw it.

However, the method of saving is flawed and data gets corrupted. When it does you'll encounter some unusual errors such as options will be grayed out when they shouldn't be or tools just wont work... general things like that.

To clear your preferences file, open Photoshop and, during the loading screen, hold down Control+Alt+Shift (Windows) or Command+Option+Shift (Mac OS). When it loads it'll prompt you to reset it.

See if that fixes the issue.

Hm, that seems to have solved it. At least for now.
Thanks!