First and foremost, this is a user to user forum provided by Adobe.
We are users just like you.
It's rare that an Adobe staff member posts on the forum, and I see a staff member moved your topic. Which means someone has noticed, at least.
I've been using every inception of InDesign since CS2 and I've never encountered your issues. That's not to say your issues are not legit, of course they are, I just never encountered them since using the software since 2006.
I'm sure someone will be along that has encountered these issues to point you in the direction for a fix.
But until then - welcome to the fourms and I hope someone can help you.
Can you let us know your
Version of InDesign
Any other information (like do you save to a server or another drive or an external drive)?
Have you taken a look at the start of the forum for the FAQ and fixes posted there for most common issues.
One thing I can tell you is that sometimes opening an older version InDesign file directly to a new version of InDesign can cause some hiccups.
I'd recommend you export your File to IDML - open that and resave it to a new file.
I have no answers for your #2 problem -- I've never encountered, that, either -- but #1 is normal for a converted legacy file. InDesign files are a database, far more complex than most other files you've been working with, and the format changes a bit with each new version of InDesign. As you probably know, .indd files are not backward compatible -- you can't open your CC 2015 files in CS5, or even in CC 2014 without first converting to IDML and risking some loss. Since the very beginning InDesign has treated converted files as "new" copies (like you get when you open a template) to prevent accidental overwriting of the original and thus making it no longer usable in its original version. Since this file is considered "new" it doesn't actually have an original folder until ist has been saved once in the current version. At that point the behavior you expect will resume.