This may happen if the trim is not set correctly, if the ladder peaks are too low, or if there are extra or missing peaks. First check the trim is set correctly. You may then need to manually call the peaks as follows:
1. Disable viewing all trace dyes except your ladder.
2. Enable the 'Show Traces', 'Show Peak Calls' and 'Show Peak Labels' options, and increase the Y scaling to its maximum extent so you can clearly see the peaks, and increase the X scaling so the peaks are wider.
3. Add missing peak calls by clicking the point where the peak call is and then clicking the 'Add Peak' button in the toolbar. Remove extra peaks by selecting the peak and clicking the "Remove Peak" button in the toolbar. Check for stutter peaks and remove the shorter of the pair. After you've edited several peaks, Geneious will recognise what ladder it is. You'll see the name of the ladder under the dye name in the panel to the right.