Alpha cocoa locks when I go with Go To Line in the search menu and similarly with the mark menu (no mark can be set and then Alpha locks). I have re-installed Alpha several times from scratch but the problem remains. I am working with an iMac (21.5inch, late 2015) running OsX 10.11.6 El Capitan. I have also AlphaX 8.2.3 on this computer which works perfectly.
I don't have this problem. Both Go To Line and Set Mark pop up a new window and it works well.
MacPro 2015 under Catalina 10.15.4.