I've found several discussions on this issue and have done everything that MuffinGroup suggested i.e., increase max_var_char in php.ini and had our hosting company clear the server cache (actually this happens every 2 hours on a script) and the custom CSS is only working for what we had in place before the latest wordpress update 4.4.
I've added custom css right on the main page in the section at the bottom that is page specific and not site wide. It works for the elements that were entered before the 4.4. update but not on anything new.
Not sure if it has anything to do with he update or not but just want to include that for diagnosis.
Any help is greatly appreciated!