Sometimes I have a problem when I cut and paste the coordinates into the line after I type /way. But if I enter them manually it works fine. Haven't figured out why yet.
I deleted the entire UI, and all uisettings, and redid everything from scratch and it works again. it's something in the uisettings xml file. Now everything still doesn't look right, but /way is worth almost anything but the default ui. If you are having a problem with 'copy/paste some say it is the 'spaces' in the copy.
My /way is working. I almost always copy/paste but I am very careful about the copy step. That all said, I've never heard of not using commas so while I don't think that is likely to be the problem for the OP it's interesting to me that it works at all.
The x seemed to work for me when I was going about to get the port points, but the little yellow line really didn't always correspond with it.
^^ This happened to me a ton. I assumed that it had to do with being way up on one of the platforms (House Yrzu area).