How many custom symbols did you import and how large (width and height in pixel) are these symbols?
Try the following:
If the custom symbol now remains in the palette, you are probably running out of memory with all the customs symbols in the palette. In this case, the advice from How can I prevent 'Out of Memory' errors in yEd? may help.
Alternatively, store fewer or smaller images in your palette section.
If the custom symbols are not properly displayed after step 6 above, your palette file got corrupted somehow. In this case there is no way to retrieve your symbols from said palette file. You will have to import the image files once more.
Unfortunately, the stacktrace probably will not help. However, one of the corrupted palette GraphML files might shed some light on this problem. Do you mind uploading one here? Please see How to upload files to yEd Q&A? for instructions on uploading files.