OK, so here's what I'm a fan of doing:
On your workflow for entry conditions for the nurture campaign, send email one there, not in the engagement stream.
Think of it this way:
Smart List = triggers to put a lead into the flow.
Flow:
Wait 1 day
Remove From Flow If In Smartlist (disqualification reason)
IF <conditions met for email 1> Send email 1 ELSE <send no email>
Add to List: Next Engagement Run
Smart Campaign: Load New Candidates:
Wait 1 week
Remove From Flow If In Smartlist (disqualification reason)
Add to engagement Program: This Program , Stream <starts with email 2>
Remove from List: Next Engagement Run
Schedule: Every Week, 1 hour after your engagement program runs
Here's why: A nurture program is not a quick win. You shouldn't use it expecting quick turn-around. If you do it correctly, your stream pace should be 3-4 weeks apart.
Now, obviously you don't want the person to wait a month to get their first email from you so you send the first email within a day or two of the person qualifying for Nurture, then wait a week and drop them in. This way, Email 2 never comes closer than 2 weeks from the date of email 1. If you run Nurture on Thursdays at 6am, the lead gets loaded in the next coming Thursday at 7am. If Nurture is running that day, oh shucks- just missed the run date.