There are two options. First, you may restart chosen isolated application as non-isolated by caption context menu.

Note, restart is required because an isolated application can not be merely switched to non-isolated state without security breach.
Second, you can enable pop-up dialogs again by following steps:
1) open GeSWall Console from Programs\GeSWall\GeSWall Console menu of
Start button
2) go to "Applications" folder
3) select the application for which you have disabled pop-up
4) Right button mouse click, properties menu item

5) set "Security Level" from "Trusted, auto-siolation" to Trusted and
press OK.
