problem with upper and lower cases

It sounds as if your EndNote preferences are set to automatically add journal names  to the Journals Term list. If entries get into this list in the wrong case or as abbreviations: this is what you will be offered by autocomplete. It is easy to go to edit the Journals Term list, with your EndNote library open, go to Tools, then Open Term List and select Journals term list from the list of options. Find the entry you want to change, and with it highlighted click the “Edit Term …” button, correct the entry in the full title box and then click OK to save changes. Occassionally OK will be grayed out, the easiest way to make it active is to put an abbreviation in the first abbreviate title box.