One thing that can mess up workspaces on a mac is if you make any adjustments to the Arrangement settings in System Prefs-Monitors. I have found that any small adjustment to the alignment between monitors there can result in windows stacking up behind the project arrangement window on my main screen for all project saved under a previous alignment. For me, this is easily solved by saving a new adjusted workspace and hitting it’s shortcut. Once the project is saved again it spreads out properly when opened.
Also, I’m not at my workstation right now, but I think there are two types of workspaces - global and project. It could be that your project workspace is overriding the global one you are setting. Maybe.