As per DS4Windows website:
It's possible that MS really wants you to use XBone controller instead of Sony's offering.
You might want to hold off with upgrading to see if the issue gets resolved. It's not like you don't have a year to do so.
//EDIT:
Straight from DS4Windows maker:
Emphasis mine.
//EDIT2: Temporary workaround found:
Note: same games work with the DS4 without DS4Windows (however it does use rumble etc.) Games like these can cause double input in menus (ie pressing down on the dpad moves 2 spaces) or the wrong button to do incorrect functions. To solve this, check Hide DS4 in the settings, if you see a warning in the log/text on the bottom, that means you must close said game or client that causes the conflict and reconnect the controller. (Note: Hide DS4 currently does not work in the Windows 10 Preview (very likely won't work with RTM, I'm not certain how to go about fixing this yet))
It's possible that MS really wants you to use XBone controller instead of Sony's offering.
You might want to hold off with upgrading to see if the issue gets resolved. It's not like you don't have a year to do so.
//EDIT:
Straight from DS4Windows maker:
Hey guys Im the dev of DS4Windows, basically the case is that there was a local service on Windows 7 - 8.1 that made sure the System didn't grab every device the moment it connected. Now that it's missing, the system keeps the DS4 Controller (Wireless controller) visible and still active, and being the system, it notices the controller before DS4W can hide it.
It won't affect every game, just games that support dinput, such as Dark Souls 1, Distance, and pretty much every game made in Unity. Like I said on the site, I have no idea how to fix this yet, when Windows 10 officially comes out I'll look into this more, but having tried the build of WIndows 10 likely to be the official RTM build, it seems like it will remain to be a problem.
Also sorry for the lack of updates, I've been pretty busy. I'll will be (hopefully) try to add Chinese support and some new features soon, but being perfectly honest, if I or anyone can't find a way to hide the controller on Windows 10, I can't say I'll be supporting DS4W for much longer.
Emphasis mine.
//EDIT2: Temporary workaround found:
Bear in mind this is only a temporary fix until a proper solution comes around. It is rough, and far from ideal.
Right, so I have only tested this with Dark Souls 1 so far. Currently testing DS2 SOTFS (it is 64bit, so it's a bit strange.) As I do not really know of any other games which require the Hide Controller option, I can't test with those. But they SHOULD work with this method.
1. Plug in your DS4 to your PC as you always would and launch InputMapper/DS4Windows as Admin (I use DS4Windows).
2. Hiding the controller/using exclusive mode must be enabled (actually, it might not be necessary but all I know is that it works with it on).
3. Download x360ce.
4. Open the ZIP and place the single .exe into the folder where your game .exe is.
5. Launch x360ce.exe which you moved into your game folder as an Admin.
6. It should ask if you want to create the ini and dll files required to make it work. Say yes to both.
7. It should then ask if you want to use the internet to automatically search for settings. Select that option. Then click finish.
8. This is a repeat of step 7 because it detects 2 controllers due to the way InputMapper/DS4Windows works.
9a. x360ce should detect 2 controllers now: Controller 1 should be "Wireless Controller", and Controller 2 should be "Controller (XBOX 360 For Windows).
9b. This might be optional, but to be sure, open Game Controllers in the bottom right of x360ce, then click Advanced and make the "Controller (XBOX 360 For Windows)" as your preferred device.
10a. Back in x360ce, click the Options tab (just to the right of Controller 4) and select "Enable Combining".
10b. Go back to the Controller 1 tab and click on the Advanced tab. Check "Combine this Controller".
10c. Go to the Controller 2 tab and click on the Advanced tab. Check "Combine this Controller".
11. Click Save, and then close x360ce. You don't even need it open when you play your games, just for that first time setup.