Within the 2005-2010 campaign aimed at extending the coverage of quality regional journals, Thomson Reuters started indexing a large number of journals published among else in Southeast Europe (SEE). In this study we looked at the range and effects of this expansion. The number of national journals indexed in JCR was related to the national performance in WoS calculated in two ways: as it is and as corrected for the contribution of national journals. The study included 14 countries. All data were downloaded from WoS. The period from 2007 to 2010 was covered. It was found that, as a result of the campaign, coverage of various SEE countries became highly uneven. It was also found that the increment in coverage poorly corresponds with the potentials of various national research communities, as measured by the Relative Citation Index (RCI). Corrected performance, calculated by omitting national journals from each country's output, did influence the publication and citation rate of SEE countries, but not to the degree of changing country rankings on the two measures. However, it produced substantial changes in ranking on RCI, suggesting that overrepresentation has serious practical consequences on the bibliometric status of countries from the region. Decline in RCI rankings was observed among those overrepresented countries that published journals of lower internationality and Impact Factor. The results generally suggest that overrepresentation in WoS/JCR is not in the long-term interest of both awarded countries and Thomson Reuters itself.