Windows 10 is ignoring my file associations

Microsoft just doesn't understand how annoying they are when they mess with my computer. I have put up with all kinds of weirdness with Windows 10, but thanks to Classic Shell and Spybot Anti Beacon I feel I am at least partially in control of my own PC. Until recently.
I started noticing some weirdness with my file associations. I've learnt to put up with the occasional file association reset that Windows Update does, trying to force me to use Edge to open PDF files instead of Acrobat. That's a well known and much hated "feature" of Windows 10. But this is different: it's a stubborn refusal to pay any attention to the fact that I don't want to edit text files with Notepad. I use EditPad Pro, and when I check in the registry it is correctly set up to use EditPad Pro. Except that the desktop ignores this completely. It seems that Windows Explorer (that's explorer.exe not Internet Explorer) is loaded is some weird mode when Windows 10 boots up. Any text file on the desktop will open in notepad. Any folder I navigate to from the desktop, such as via "This Computer" or via the "User's Files" icon is also affected.
I noticed an important exception: I have a batch file that opens my TrueCrypt drives and then runs the following command:
start explorer.exe X:\dev
which opens the X:\dev folder on the TrueCrypt drive. This version of Explorer gets the file associations correct every time. Some further experimenting has led me to a simple, but weird, workaround:

• Allow Windows 10 to boot up and stabilize as normal.
• Open the Windows Task Manager.
• Scroll down the list of tasks until you get to the "Windows Processes" section.
• Right Click on the one or two copies of Windows Explorer, and select "End Task".
• Don't panic when the desktop disappears.
• From the Task Manager go to the top menu, select File, then "Run new task".
• Type in "explorer.exe" and make sure you tick the box that says "Create this task with administrative privileges"
• Click OK.

You will get your desktop back and once it has settled down the file association problem will be gone until the next time you reboot the PC.
Like many workarounds I cannot explain why it works, only that it does. I don't know if it is something peculiar to my Windows setup, but I suspect not. If this helps you too, please leave a comment.

Update 3rd December 2016: After updating to version 1607 the problem seems to have gone away. I am cautiously optimistic.
The upgrade process turned into a bit of a mission, but after leaving the laptop to do its thing overnight I have a new version of Windows 10.