In EcoSys, many popup windows are not really popups. However, some (screen layout New Window regions and Export dialogs for example) are considered pop-up windows to the browser.
To ensure that EcoSys can create popup windows, uncheck Block pop-up windows in the Security tab of Safari > Preferences.
New Windows Opening in Screen Layout
For screen layout event setting that are supposed to open a target panel in new window, if the Open pages in tabs instead of windows setting in Safari Preferences is set to any option other than Never, Safari will open a target panel in a new tab. To launch a new window, select Never.
Vertical Scroll Bars
In Safari, the vertical scroll bars are usually hidden and only visible briefly when a list is first displayed and while you are actively scrolling through the list.