As in the title. To reproduce (testing in Jabref 2.6):
1) Mark some entries
2) Search using IEEE or ACM tools
3) Import some of the results
4) You see the new imports as marked (a very nice feature) but your old marked entries get unmarked (either hand marked or from previous imports)
Expected behavior: new imports get marked and added to the previously marked entries
Thanks and best regards
This behaviour can be changed under Options -> Preferences -> General. There is one checkbox for marking newly imported entries, and another one for unmarking previously marked entries. These together can give you the behaviour you want, or like you're observing, making only the latest imported entries being marked.
Nevertheless, this option should be unchecked by default.