Use the built in multi-point tool to do the counting. It does not have this problem. In the following screenshot I used it to count the three types of objects in an image. Use the “Point Tool” dialog, opened by double clicking on the multi-point tool icon, to switch between counters. The “Counts” table, opened by typing “y” (Edit>Selection>Properties), displays the counts. The “Results” table, opened by typing “m” (Analyze>Measure), shows the counter associated with each point.
You should be running ImageJ 1.51g, or later, which fixes a bug that sometimes caused counting to fail when switching between counters. The 1.51h4 daily build adds the ability to display the counters and counts in the Results window.