Not sure if you ever discovered an answer to this yet, but in case you or other people haven't figured it out... I know exactly what you're talking about, but it's not just with the Seaboard. Check which Input you're using on the track that you're recording on. You have to make sure you have selected the exact Seaboard (or any other MIDI controller) that you want to use. For some reason if you leave the input set to All Inputs, it records those obnoxious little notes at full velocity.
If you've already recorded sections with them, the easy fix to keep from losing all the material is to select all of the notes, then go to Musical Functions -> Delete Notes -> Delete notes shorter than 0:00:12. That'll get rid of all of them and leave the full-size notes that don't play right as long as the little "micro notes" exist.
Hope that helps!