It does come from the Manager and it seems to appear completely at random in the current version of Revo. I don't any way to disable it without hacking the JS code.
Could you file a bug report here (if there isn't one already): http://bugs.modx.com
If you give me the *exact* message in the popup, I can probably find it for you.
Better if you post it here. I'm more likely to see it.
Not sure if this helps, but I saw this problem for the first time today on 2.2.10-pl.
I was using Articles. I had an article container open, I had created an article, saved it. Everything was fine. The save button was greyed out. So, I went to close the article container, and it gave me this error. Again the saved button was greyed out.
I changed some text and got the save button to light up, pressed save. Thought this would fix it, not luck. pressing close still gave me the error.
I finally noticed that somehow the article template field had gotten reset. It did not have a valid template selected. I selected the template, pressed save, and "Ta Da" close worked.
You may not be working with Articles, but maybe what MODX is doing, is that for some reason it thinks a required field is not entered, but it is not displaying the red text or message? Maybe if they just put a value in some field it will stop the error message. It might me a temporary work around until someone provides you a way to disable this or fix it.
Just a thought.....