Hello,
Is the issue that in your bibliography, journal article references are having their journal names abbreviated without periods, and you want it to abbreviate with periods? If this is your issue, you would want to follow the steps in this FAQ:
http://www.endnote.com/support/faqs/Styles/faq5.asp
Make sure that in step 10, you select Abbreviation 1, this is the abbreviation with periods.