Hello,
I have tested this problem on yesterday updates of Jessie and Stretch operating systems. Same problem exists in both of them. I also confirm that There is no such problem on fixes_1_6 branch aka 1.8.0RC3 version
Problem is that, when ever I open a dialog windows of Lazarus - be it open file, options, form list (Shift+F12) - that window shows up and instantly refresh itself and go behind all open Lazarus windows having focus on itself. If current windows allows, I can drag that modal window. I can use keys, or click its visible parts. Everything works. Except it stays behind no matter what.
I also cannot select a design form because Lazarus dialog is a modal one.
With these explanations, now I hope it is easier to understand it using attached pictures.
P.S. First picture, there is no problem. Just to display view before any dialog window shows.