I have opened a support incident so that someone can work with you on this issue directly. Most likely it is an issue with the library.php file which is what is used to calculate the paths. We have updated that file based on support issues on some servers and that is probably what you are running into. I have attached a new version of that file to this thread. You can try finding and updating the file wherever it appears in the sites you are having trouble with (it may appear more than once).
Update the support incident if you are able to solve the issue on your own, or update it with a phone number and we can help you debug and find a solution.