Well for starters at f/4.5 you're already in the slow territory. A lot of cameras may tend to conk out at f/5.6 or above, but with a slow lens like that you're already low on light.
I assume your ND grad filter will be used to block the sky mostly, depending on how you are using it. Unless you're filter is crap and noticeably not sharp then all it can do is reduce either the contrast at the focus point, or the amount of available light for focusing.
Is the focusing slower in darker overcast conditions than in the light? Typically the amount of available sharp contrasty light that gets to the AF defines the performance.