The standing you get from an agent is related to the:
- Your Social skill level
- Corporation of the Agent (different corps under the same faction might give different standings)
- Corporation Size
- Level of Agent
- Enemy of the Mission (i.e. Recon against guristas might give different standing than Recon against Blood)
So, in your case, check which of the above where different at the time you run the mission.
What I am certain of, is that if you run the same mission for the same agent again, you will get the same standings.
And some additional info if you want to get technical: