Finally! I've made it work by setting a progressive video mode first, maybe some settings were borked in the emulator itself or I don't know, because at my first tries it didn't work, maybe I wasn't setting a progressive one, well whatever.... I've set a progressive mode as default for the desktop and now it does switch in the emulators. I'm pasting my settings in Fusion here (the only thing I don't like is that it has a small blue letterbox in the upper and lower sections of the screen)
Fusion.ini:
;---------------------------------
; Graphics Compatibility Options
;---------------------------------
ForceCompatibleGFX=0
CompatibleGFXOpt=1
EnhancedGFXOpt=0
ForceFullScreen32=0
VistaAeroIgnore=1
VistaNoWndVSync=1
DebugFlags=0,0,0,0
;---------------------------------
; Expert Options [DANGER! RTFM!]
;---------------------------------
RefreshRate60Hz=60
RefreshRate50Hz=50
UseExpertModes=1
UseAutoSwitching=1
MinSwitchDelay=100
Mode256x240=256,240,60,50,256,240
Mode256x480=256,480,60,50,256,480
Mode320x240=320,240,60,50,320,240
Mode320x480=320,480,60,50,320,480
So yeah, I can't switch from interlaced to progressive using an HD 4350 under Win7 without it dying, it would do great for an update if you fix this.
Thanks a lot for your help and for these wonderful drivers Calamity!!

Oh yeah, also, under Win8 you need to apply configuration fixes to the ddraw dll to make it work properly, check here
http://classicgamefixes.wix.com/home#!kega-fusion/c4dr
(stuff like this is why I installed windows 7 instead)