Dither no less frequently than every 3 frames. The fewer frames you stack, the more often you should be dithering. For longer exposures (over 5 minutes), you should be dithering every frame since the dithering overhead will be smaller. Dither aggressively. A couple arcseconds difference is nothing....you probably are not dithering enough. When dithering occurs, you should see fairly large spikes in your guide graph. The star should move anywhere from a couple arcseconds to 6, 8, 10, 12 arcseconds, in both axes. Dithering in a single axis is less than useless, as it can actually CAUSE correlated (walking, raining) noise!! Always dither both axes.
Dithers should not take a long time to settle. Anywhere from 5-10 seconds, maybe slightly longer if it was a large dither. If it is taking you 40 seconds, a minute or longer to settle, then you have something misconfigured. Settling factors are usually in pixels...so if it says something like settle at 0.25, that would be one quarter of a pixel. If your guide RMS is say, 0.7 pixels, then trying to settle at 0.25 pixels is only going to happen by luck...on the off chance...and it will take FOREVER. Settle at no less than 0.7 pixels, maybe slightly above, to ensure that settling occurs efficiently.