I tried using Ipe for graphs, the move graph nodes feature works great, but then I encountered the problem that when I save my file (as .pdf or .ipe) and then reopen it, the feature works 50% of the time, very often only the node is moved.
I asked some people to test and on their machines this works (maybe a problem only on fedora, but this does not make sense).
I am using Ipe 7.2.26 on Fedora 38 (tested also on 7.2.28 on another machine using Fedora 39 and It also does not work). I also tried on a windows machine and there the feature seems to work after reopen (but I prefer Linux so that is not an option).

I do not think that I am doing something wrong because the feature works perfectly before reopening the file.
Let me now if you need any other information.