Hi silmalik,
It seems that you have generated the patch by referencing the root folder, thus patch level shifted up by one level according to my test. I mean, "patch -p1" doesn't work inside of the source tree (but -p2 does) . Probably you have to compare them in same folder like:
cd /
diff -Naur mednafen emu4crt > emu4crt.patch
I didn't notice any worrying delay and glitch issues during resolution switches.
Regards.
 Initializing sound...
  Using "ALSA" audio driver with device "sexyal-literal-default":
   Format: 16 bits(signed, 2 bytes, little-endian)
   Rate: 48000
   Channels: 2
   Buffer size: 1536 sample frames(32.000000 ms)
   Latency: 1536 sample frames(32.000000 ms)
   Period size: 512 sample frames(10.666667 ms)
    Warning: Period time is too large(it should be <= ~5.333ms).  Video will appear very jerky.
 Initializing video...
### VIDEO Native resolution init - set to 640x480
  Driver: OpenGL
  Display Mode: 640 x 480 x 24 bpp @ 30Hz  (Window: 640 x 480)
  Shader: none
  Fullscreen: Yes
  Special Scaler: None
  Scanlines: Off
  Destination Rectangle: X=0, Y=0, W=640, H=480
  OpenGL Implementation: X.Org R300 Project ATI RV370 2.1 Mesa 17.2.4
  Checking extensions:
   GL_ARB_texture_non_power_of_two found.
   GL_ARB_sync found.
  Using non-power-of-2 sized textures.
  Checking maximum texture size...
   Apparently it is at least: 2048 x 2048
  Using GL_BGRA, GL_UNSIGNED_INT_8_8_8_8_REV for texture source data.
PSX GPU - Startup resolution change bypass (1).
PSX GPU - Startup resolution change bypass (2).
PSX - GPU register - resolution change to: 640x480 (V=39)
 Initializing video...
### VIDEO Native resolution init - set to 640x480
  Driver: OpenGL
  Display Mode: 640 x 480 x 24 bpp @ 30Hz  (Window: 640 x 480)
  Shader: none
  Fullscreen: Yes
  Special Scaler: None
  Scanlines: Off
  Destination Rectangle: X=0, Y=0, W=640, H=480
  OpenGL Implementation: X.Org R300 Project ATI RV370 2.1 Mesa 17.2.4
  Checking extensions:
   GL_ARB_texture_non_power_of_two found.
   GL_ARB_sync found.
  Using non-power-of-2 sized textures.
  Checking maximum texture size...
   Apparently it is at least: 2048 x 2048
  Using GL_BGRA, GL_UNSIGNED_INT_8_8_8_8_REV for texture source data.
MAIN - native resolution switched
PSX - GPU register - resolution change to: 320x240 (V=17)
 Initializing video...
### VIDEO Native resolution init - set to 320x240
  Driver: OpenGL
  Display Mode: 320 x 240 x 24 bpp @ 50Hz  (Window: 320 x 240)
  Shader: none
  Fullscreen: Yes
  Special Scaler: None
  Scanlines: Off
  Destination Rectangle: X=0, Y=0, W=320, H=240
  OpenGL Implementation: X.Org R300 Project ATI RV370 2.1 Mesa 17.2.4
  Checking extensions:
   GL_ARB_texture_non_power_of_two found.
   GL_ARB_sync found.
  Using non-power-of-2 sized textures.
  Checking maximum texture size...
   Apparently it is at least: 2048 x 2048
  Using GL_BGRA, GL_UNSIGNED_INT_8_8_8_8_REV for texture source data.
MAIN - native resolution switched
PSX - GPU register - resolution change to: 368x240 (V=64)
 Initializing video...
### VIDEO Native resolution init - set to 368x240
  Driver: OpenGL
  Display Mode: 384 x 240 x 24 bpp @ 50Hz  (Window: 384 x 240)
  Shader: none
  Fullscreen: Yes
  Special Scaler: None
  Scanlines: Off
  Destination Rectangle: X=8, Y=0, W=368, H=240
  OpenGL Implementation: X.Org R300 Project ATI RV370 2.1 Mesa 17.2.4
  Checking extensions:
   GL_ARB_texture_non_power_of_two found.
   GL_ARB_sync found.
  Using non-power-of-2 sized textures.
  Checking maximum texture size...
   Apparently it is at least: 2048 x 2048
  Using GL_BGRA, GL_UNSIGNED_INT_8_8_8_8_REV for texture source data.
MAIN - native resolution switched
PSX - GPU register - resolution change to: 320x240 (V=17)
 Initializing video...
### VIDEO Native resolution init - set to 320x240
  Driver: OpenGL
  Display Mode: 320 x 240 x 24 bpp @ 50Hz  (Window: 320 x 240)
  Shader: none
  Fullscreen: Yes
  Special Scaler: None
  Scanlines: Off
  Destination Rectangle: X=0, Y=0, W=320, H=240
  OpenGL Implementation: X.Org R300 Project ATI RV370 2.1 Mesa 17.2.4
  Checking extensions:
   GL_ARB_texture_non_power_of_two found.
   GL_ARB_sync found.
  Using non-power-of-2 sized textures.
  Checking maximum texture size...
   Apparently it is at least: 2048 x 2048
  Using GL_BGRA, GL_UNSIGNED_INT_8_8_8_8_REV for texture source data.
MAIN - native resolution switched