iTunes Issues (surprise-surprise)

This is a two part problem.

First Problem:

When I sign in to my account through iTunes, all of the songs I have previously "unchecked", (whilst signed out) in my library then become "checked". Is there a reason that this is happening? Also I should mention, whilst I'm signed in to my account, I then proceed to uncheck the songs again.

Second Problem:

"Skip when shuffling" - is this a feature that actually works any more? Mine certainly doesn't. As much as "Tears in Heaven" is one of the best songs ever made, iTunes seems to think I want to listen to it, followed by "Turn Down for What", every time I turn shuffle on. I really don't.

Any advice would be greatly appreciated, unless of course it's "Delete the music you've unchecked/don't want to listen to on shuffle" - that's not constructive or helpful to anyone.

Cheers in advance.