Not sure what you mean by not smooth. Maybe you have the v-sync on and the refresh higher than 60hz - The real GBA runs a 60hz. I had this problem too. I fixed this by setting DirectX 640x480 res to lock at 60hz - then I set the emu to use fullscreen @ 640x480 - bam, problem solved. The game are no longer jerky @ 100% FPS like before. BTW, I set almost all my emus up like this and they run/scroll much smoother. The only EMU's that don't seem to be affected by this are PJ64 and EPSXE.
System:
AMD XP 2000
256meg 333mhz DDR
MSI KT333 Ultra2
Geforce ti 4 4400
80gig,40gig,40gig all @ ATA 100 - 7200rpm
Winxp Pro and win98se
SB Audigy
32x cdrw 8x DVD