On which operating system are you using yEd?
Do you still know which former version you were using that did not exhibit this problem? (By the way, yEd 3.18.2 works as intended for me.)
Can you upload a GraphML file with one or more of the problematic groups?
Please see How to upload files to yEd Q&A? for instructions on uploading files here.
Have you tried if the most current version (220.127.116.11 at the time of this writing) behaves the same?
Regarding your "I have 10 group nodes, labeled 1..5 with a +/- for each of them." statement, only the nodes with a "-" symbol are group nodes. The others are folder nodes (i.e. closed group nodes).
Could it be that you actually want folder nodes instead of group nodes? In this case, simply close the groups you create with CTRL+ALT+G by clicking the "-" symbol.