If there are closely spaced alleles, the labels may not be completely displayed due to overlapping. This is common for many chemistries, including but not limited to MLPA (as shown below), MS-MLPA, MSI, Aneuploidy, Fragile X, and human identification chemistries used in forensic casework, chimerism analysis, and relationship testing.
There is an option to stagger the allele labels in different rows so they are all viewable. The images in this article are from GeneMarker, but the steps are the same for GeneMarkerHID and ChimerMarker, as well.
In the software, go to View > Preferences > Display Settings tab. Select Max Allele Label Layers and enter the number of allele label rows you would like to display below the electropherogram. Click OK. The settings should be saved for future projects.