Hey folks - thanks for bringing this to my attention. I want to make sure I understand the problem, so please bear with me!
Are you saying that when you add a secondary domain (e.g. hubspotforstartups.com) to a company (e.g. hubspot.com) and new contacts come in that are associated with that secondary domain (hubspotforstartups) then they are NOT associated with hubspot.com? That would be odd.
The only case where that might happen is if hubspotforstartups.com already existed, but was never merged with hubspot.com.