So... I found a solution. I apologize if this is something that everybody already knows or something that I already should have known.
Basically, I set the normal prescale to 1 and change the x and y prescale under hlsl to a higher number such as 4. Here is what that looks like in my config file (this is just the section of the config that matters for this fix. I've omitted the rest).
# # WINDOWS VIDEO OPTIONS # video d3d numscreens 1 window 0 maximize 1 keepaspect 1 prescale 1 waitvsync 0 syncrefresh 0 menu 0
# # DIRECT3D-SPECIFIC OPTIONS # d3dversion 9 filter 1
# # DIRECT3D POST-PROCESSING OPTIONS # hlsl_enable 1 hlslpath hlsl hlsl_ini_read 0 hlsl_ini_write 0 hlslini %g hlsl_prescale_x 4 hlsl_prescale_y 4
This seems to fix the issue entirely and also fixes the issues that I was having outside of using hlsl. So, it also fixes the missing line of pixels at the bottom that is noticeable in games such as Metal Slug. It seems like the normal d3d prescale value is giving me issues unless set to "1" but the prescale that is done under the hlsl settings works just fine.
I have tried this on both Windows 7 x64 machines that were giving me issues and it seems to work fine on both. I still don't know what was causing the original problem but hopefully this will help others with the same issue.
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