The issue with pop-up tooltips seems like background is hidden unintentionally via an addon...
Maybe :SetAlpha(1) or :SetHidden(true) is being set incorrectly by one addon while another addon is attempting to display their portion of the tool-tip. You would need to go through your addons to locate the ones that add data or handle any aspect of the tool-tips.
Is it just tool-tips of items or tool-tips of food/reagents, etc. Narrowing it down could help a lot to resolve the issue with your tool-tips as you could then further eliminate addons that process those particular tool-tips.
The issue with broken/non-functioning key-binds sounds really similar to the Esc key bug, at least to me...
Could it possibly be due to input lag when hitting the key-bind that upsets the function?
Perhaps transitioning from one item to another whilst using the key-bind is a cause to the Interact key-bind ceasing to function?
Do you get any disconnects from 'spamming'? I think it would be interesting if there was found to be a correlation between the two.
I wonder if the key-bind issue can be reproduced without addons.
Of course, due to my limited knowledge of lua I could be talking out of my arse
