I have posted this on google-apps-script-issues (https://code.google.com/p/google-apps-script-issues/issues/detail?id=4723&can=4&colspec=Stars%20Opened%20ID%20Type%20Sta
Andrew. First of all thank you as you triggered something in my mind. I went all the way bottom up and checked each script and a library it was calling. There were obviously dependencies, however nothing that should have been a problem. a couple of libraries even though in development mode seem to cause a problem. I had to create a new version but it was not enough just to update their version in other scripts. In the calling scripts I had to remove all libraries and re-add them one by one while testing whether the project properties shows up or not. I just wish Google would have a utility to clearly highlight what was wrong because I can't figure it out though I went twice through their documentation in regard to libraries and development mode. Since I have about 30 libraries or so, not to mention spreadsheets and apps it took me nearly a whole day... Thanks again!
To all, it seems that there is a problem where sometimes libraries get out of sync (at least that's the best way I can describe it). You may need to create new versions for the libraries (even though these are in development mode. And in each problematic script remove and re-add the libraries (in at lease a couple of transactions - first remove and confirm then add - and better one at the time while checking that your project properties opens properly). This solved the problem for me.