Hi Brant, this can be a timing issue.
I am reposting a forum entry here though it references WIN7 this has been an issue since then:

https://answers.microsoft.com/en-us/windows/forum/windows_7-performance/windows-7-explorer-window-does-not-appear-in-front/1199682e-2415-4a7a-bf21-f57a972122ee

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In Windows 7, window pop-ups are control by FOREGROUNDFLASHCOUNT and FOREGROUNDLOCKTIMEOUT in the REGISTRY (You need to CLICK ON the START ICON at the leftest of your TASKBAR, and type REGEDIT in the SEARCH PROGRAMS and FILES field). Go to the REGISTRY EDITOR and it is at this path:
HKEY_CURRENT_USER\CONTROL PANEL\DESKTOP.
One click on the DESKTOP (Manual Display), and your will see the detail populate at the right side of the REGISTRY EDITOR window. Go to find the FOREGROUNDLOCKTIMEOUT, and double click on it.
The EDIT DWORD small window will pop-up. Change the VALUE DATA to ZERO.
Yes, you must restart your PC in order for the change to apply.
Here is what is telling us in the Windows 7 manual: http://technet.microsoft.com/en-us/library/cc957205.aspx
ForegroundFlashCount


HKCU\Control Panel\Desktop
Data type
Range
Default value
REG_DWORD
Number of flashes in decimal
3
Description
Specifies the number of times the taskbar button flashes to notify the user that the system has activated a background window. If the time elapsed since the last user input exceeds the value of the ForegroundLockTimeout entry, the window will automatically be brought to the foreground.
Related Entries
Yes, if the DOWNLOAD timer in the FOREGROUNDLOCKTIMEOUT (SHOWING 30D40 Hexadecimal) is longer than the 3 FLASH(Default), then you will see the new WINDOW pop-up behind your mother window or your application. Set the VALUE DATA to ZERO, sooner than the 3 FLASH of the FOREGROUNDFLASHCOUT, the the DESCRIPTION above is applied.

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end of forum post

Please let me know the outcome.
Chris