Dear Leanne and Myoshigi,
Thanks for your time to respond to my question. I checked the points that both of you have raised and everything was OK, except the problem still was there. Eventually, I had to call the customer support in USA to solve this problem. Yes, John East did suggest correctly to replace the term list, but I their website failed to provide instructions how to do so. Anyway, after I solved this problem I made a quick note for myself how to do this and I am attaching it to this thread so whoever encounters the similar difficulty I hope will benefit from this.
Here is the complete procedure in text format:
How to update the Journals Terms List of EndNote version X2
Fatkhulla Tadjimukhamedov, NMSU 2008
The Journals Term List is a necessary component of EndNote program that enables to automatically update the journal names as well as abbreviation features that are predefined in Term List files (usually saved in the directory C:\Program Files\EndNote X2\Terms Lists). In order to successfully update the journal terms list the following steps must be taken, so that the program will recognize the updated list: If you are updating the journal list terms of an already built library, make sure you back up the original file. When building a new library or editing the existing library you may realize that some citations are being abbreviated accordingly, while the others are not after importing references. The reason for such inconsistency is that the Term List does not have proper Journals Term Lists set up. To fix this:
1. Go to Tools menu > Open Term Lists > Journal Term List. This will open Term Lists message dialog.
2. On the Lists tab select journals and press Delete List… button. This will delete the Journals entry. Press Create List button and type Journals in the text field. Do not forget to check the Journal List under the text field otherwise it will result in error and the new list will not be recognized.
3. Press OK button. Then press Import List button and navigate to C:\Program Files\EndNote X2\Terms Lists directory and select the desired term list. Press Open button to confirm the selection and press OK button in a message dialog prompted afterwards. Press Close button of Term Lists window. Now when you click on the references that did not use the journal title abbreviations previously, they will now show up in abbreviated format.
4. One last important step that must to be done: Go to Edit menu > Preferences and select Term Lists and uncheck the Update lists when importing or pasting references entry.