Hello, Gustavo, What Platform are you using? what OS version? What version on FMP?
Are you scripting the window(s) in some way (size, location, etc.)?
Yes, it is in MAC OS X 10.6.8
FMP Pro 12 Advanced.
Yes, I am scripting the first Window :
New Window [Name "xxx" ; height : 300; Width 150 ; Top 0; Left 150 ;
Go to Layout [ "xxx"]
Show All Records
Set Field[ xxx]
Perform Find 
Allow Formatting Bar (Off]
Then I tried to open a second window using the same parameters, of course
different window and Layout name:
New Window [Name "yyy" ; Height : 300; Width 150 ; Top 0; Left 250 ;
Go to Layout
If I'm not mistaken, it looks like you're opening up modal style windows. The second modal has the focus until you dismiss it either by closing it or scripting away from it
I tried changed both Layout to the Style : Floating Document, and Adjusting size and location to get the second one at the right position.
Now I have both Layouts side by side, that's what I wanted.