Mouse lag but FPS is stable in Direct3D 9

[EliasFrost]

Hi again, making a lot of threads lately...

I'm having a bit of an issue at the moment, I'm trying to run my game steadily in Direct3D but I'm faced with a problem that I don't know how to solve, mainly because I don't know what is causing it. When I run the game in DirectDraw, it works fine with no mouse lag but when I run the game in Direct3D (as I intend) I get this really jerky lag, not acceleration, legit lag and I don't know how to fix it, it becomes very apparent when I have multiple GUIs visible at once. But the strangest thing is that the FPS is steady at 40 all through my test, so why does the mouse lag?

I'm running the game at 640x400

Oh and I'm running it on win7 64x

Thanks!