When using fullscreen with Direct3D and 'emulate fullscreen' turned off, the video won't stretch itself in fullscreen but instead will just stay a smaller size and shove itself in the top right corner of the screen. This bug only appears in 1.53 as I went back and tested 1.52 and it does fullscreen just fine (with same settings). Also, I can confirm this bug happened on at least two different computers. One 32-bit and the other is 64-bit on Windows XP and Windows 7, respectively.

Could you try if this interim build fixes the issue?
http://download.sessionclan.de/overfiend/snes9x/testbuilds/snes9x_testbuild_29042011.zip

The new build fixed that bug, but I think it created a new one. Now when using fullscreen the windows taskbar flickers in the background like a strobe light when 'maintain aspect ratio' is enabled. This happens when I use 1280x800 32-bit 60hz, but 1280x800 16-bit 60hz doesn't have any problems at all. I tried to reproduce this bug on my Windows 7 computer and no problems.

I can confirm the blinking task bar bug. Windows 7 32bit at 720p 32-bit 60Hz it happens for me. Its and Nvidia video card. On my Intel video laptop The problem is non existent as for as I know. What video card do you have MadClown?

The computer that has the flickering probem is using an ATI mobility 9700 on Windows XP, but my other computer is using an Intel GMA 4500MHD on Windows 7 and isn't having any taskbar flickers at all.

Could you try if this fixes the flickering:
snes9x_testbuild_07052011.zip

Well I just tested the 07052011 build and so far so good. No flickering anymore. Thanks very much!