PS4 Controller no longer working with Citra

I normally use my PS4 controller connected with DS4Windows to play games with Citra and it has worked fine in the past. Today when playing a game, the controls randomly stopped working midgame.
I tried resyncing the controls, but none of the inputs will register when doing so. It works fine when syncing inputs with my keyboard instead.
I have tried installing multiple older versions of Citra and have also completely uninstalled and reinstalled the program but nothing has changed. I tried updating DS4Windows and using an older version in case there was an issue there but that had no effect.
The controller works fine when used in all other programs on my PC, but I can’t figure out how to fix this problem with Citra. Anybody have any ideas?

Diagnostic Log:
[ 0.006004] Config core/settings.cpp:LogSettings:78: Citra Configuration:
[ 0.006024] Config core/settings.cpp:operator():75: Core_UseCpuJit: true
[ 0.006035] Config core/settings.cpp:operator():75: Core_CPUClockPercentage: 100
[ 0.006035] Config core/settings.cpp:operator():75: Renderer_UseGLES: false
[ 0.006036] Config core/settings.cpp:operator():75: Renderer_UseHwRenderer: true
[ 0.006036] Config core/settings.cpp:operator():75: Renderer_UseHwShader: true
[ 0.006037] Config core/settings.cpp:operator():75: Renderer_SeparableShader: false
[ 0.006037] Config core/settings.cpp:operator():75: Renderer_ShadersAccurateMul: true
[ 0.006037] Config core/settings.cpp:operator():75: Renderer_UseShaderJit: true
[ 0.006038] Config core/settings.cpp:operator():75: Renderer_UseResolutionFactor: 1
[ 0.006043] Config core/settings.cpp:operator():75: Renderer_FrameLimit: 105
[ 0.006043] Config core/settings.cpp:operator():75: Renderer_UseFrameLimitAlternate: false
[ 0.006044] Config core/settings.cpp:operator():75: Renderer_FrameLimitAlternate: 200
[ 0.006044] Config core/settings.cpp:operator():75: Renderer_VSyncNew: true
[ 0.006044] Config core/settings.cpp:operator():75: Renderer_PostProcessingShader: none (builtin)
[ 0.006045] Config core/settings.cpp:operator():75: Renderer_FilterMode: true
[ 0.006045] Config core/settings.cpp:operator():75: Renderer_TextureFilterName: none
[ 0.006046] Config core/settings.cpp:operator():75: Stereoscopy_Render3d: 0
[ 0.006046] Config core/settings.cpp:operator():75: Stereoscopy_Factor3d: 0
[ 0.006047] Config core/settings.cpp:operator():75: Layout_LayoutOption: 3
[ 0.006047] Config core/settings.cpp:operator():75: Layout_SwapScreen: false
[ 0.006048] Config core/settings.cpp:operator():75: Layout_UprightScreen: false
[ 0.006048] Config core/settings.cpp:operator():75: Utility_DumpTextures: false
[ 0.006048] Config core/settings.cpp:operator():75: Utility_CustomTextures: false
[ 0.006049] Config core/settings.cpp:operator():75: Utility_UseDiskShaderCache: true
[ 0.006049] Config core/settings.cpp:operator():75: Audio_EnableDspLle: false
[ 0.006050] Config core/settings.cpp:operator():75: Audio_EnableDspLleMultithread: false
[ 0.006050] Config core/settings.cpp:operator():75: Audio_OutputEngine: auto
[ 0.006050] Config core/settings.cpp:operator():75: Audio_EnableAudioStretching: true
[ 0.006051] Config core/settings.cpp:operator():75: Audio_OutputDevice: auto
[ 0.006051] Config core/settings.cpp:operator():75: Audio_InputDeviceType: 0
[ 0.006052] Config core/settings.cpp:operator():75: Audio_InputDevice: Default
[ 0.006052] Config core/settings.cpp:operator():75: Camera_OuterRightName: blank
[ 0.006052] Config core/settings.cpp:operator():75: Camera_OuterRightConfig:
[ 0.006053] Config core/settings.cpp:operator():75: Camera_OuterRightFlip: 0
[ 0.006053] Config core/settings.cpp:operator():75: Camera_InnerName: blank
[ 0.006054] Config core/settings.cpp:operator():75: Camera_InnerConfig:
[ 0.006054] Config core/settings.cpp:operator():75: Camera_InnerFlip: 0
[ 0.006055] Config core/settings.cpp:operator():75: Camera_OuterLeftName: blank
[ 0.006055] Config core/settings.cpp:operator():75: Camera_OuterLeftConfig:
[ 0.006056] Config core/settings.cpp:operator():75: Camera_OuterLeftFlip: 0
[ 0.006056] Config core/settings.cpp:operator():75: DataStorage_UseVirtualSd: true
[ 0.006056] Config core/settings.cpp:operator():75: DataStorage_SdmcDir: C:\Users\2906k\AppData\Roaming/Citra/sdmc/
[ 0.006057] Config core/settings.cpp:operator():75: DataStorage_NandDir: C:\Users\2906k\AppData\Roaming/Citra/nand/
[ 0.006057] Config core/settings.cpp:operator():75: System_IsNew3ds: true
[ 0.006058] Config core/settings.cpp:operator():75: System_RegionValue: -1
[ 0.006058] Config core/settings.cpp:operator():75: Debugging_UseGdbstub: false
[ 0.006059] Config core/settings.cpp:operator():75: Debugging_GdbstubPort: 24689
[ 0.277769] Input input_common/udp/client.cpp:StartCommunication:207: Starting communication with UDP input server on 127.0.0.1:26760
[ 0.693187] Frontend citra_qt/main.cpp:GMainWindow:190: Citra Version: Nightly 1721 | HEAD-89410c1
[ 0.693199] Frontend citra_qt/main.cpp:GMainWindow:206: Host CPU: Intel(R) Core™ i7-9750H CPU @ 2.60GHz | AVX2 | FMA
[ 0.693224] Frontend citra_qt/main.cpp:GMainWindow:208: Host OS: Windows 10 (10.0)
[ 0.790583] Service.FS core/file_sys/ncch_container.cpp:Load:242: Secure1 KeyX missing
[ 0.790591] Service.FS core/file_sys/ncch_container.cpp:Load:256: Secure2 KeyX missing
[ 0.790601] Service.FS core/file_sys/ncch_container.cpp:Load:347: Failed to decrypt
[ 0.790608] Service.FS core/file_sys/ncch_container.cpp:Load:242: Secure1 KeyX missing
[ 0.790609] Service.FS core/file_sys/ncch_container.cpp:Load:256: Secure2 KeyX missing
[ 0.790615] Service.FS core/file_sys/ncch_container.cpp:Load:347: Failed to decrypt
[ 0.790742] Service.FS core/file_sys/ncch_container.cpp:Load:242: Secure1 KeyX missing
[ 0.790746] Service.FS core/file_sys/ncch_container.cpp:Load:256: Secure2 KeyX missing
[ 0.790751] Service.FS core/file_sys/ncch_container.cpp:Load:347: Failed to decrypt

In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.

Do you perhaps have Steam running in the background? Steam can also provide controller drivers so it sometimes conflicts with DS4Windows.