I've never had this problem but ANY of my sitewide links that are set to open in 'New Window' are suddenly not being respected and I just cannot seem to find out why. I can't say 100% it is Gantry5 issue but I have to start somewhere and additionally I have asked JCE, as that's being my editor of use on my site to date. I've chosen none JCE editors and granted they also (TinyMCE) don't respect a given links 'New Window' either (even after clearing site and browser cache) and instead opens in the current window... it's bugging the heck out of me.
Do you have any reports at all in latest Gantry5 of it doing the above?
I tested this with tinyMCE and latest Gantry 5 and its working fine for me... the problem is somewhere else, i would suggest to disable all extensions and turn them one by one ... starting with page builder one ...