Question: are you certain the issue is related to the security settings? Rather, are you able to run the original build with App Signing disabled?
There are 4 relevant states you could end up in when trying to launch an app on OS X 10.8.
1. The app launches without any messages.
2. Gatekeeper warns you that an app is unsigned, but allows you to open it anyway. You get a "cancel" and "open" button.
3. Gatekeeper blocks the app because it is unsigned. You get a "cancel" and "move to trash" button. This can by bypassed by right clicking on the executable and clicking Open, which results in state 2.
4. Gatekeeper fubars with a message saying <appname> is damaged and can't be opened, followed by a "cancel" and a "move to trash" button. This will not be bypassed by right clicking and selecting open.
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The when we launch Starfarer for the first time with Gatekeeper set to Allow applications downloaded from: Mac App Store and identified developers (10.8 default setting), we're supposed to get (3), which can be bypassed by right clicking. We don't. Instead, we're getting (4).
Changing the Gatekeeper setting to Allow applications downloaded from: Anywhere causes (2) when attempting to launch Starfarer for the first time. Launches after that result in (1), which is the expected behaviour because Gatekeeper only applies to the first run of an executable. Changing Gatekeeper back to the anally retentive Allow applications downloaded from: Mac App Store and identified developers setting still allows Starfarer to be launched afterwards, because the executable has now been marked "safe" by Gatekeeper.
The updated build fails to launch with a (3) with Gatekeeper strict, and launches with a (2) with Gatekeeper relaxed, which is the appropriate behaviour for an unsigned app.
Hope that helps.
---edit---
Would changes precisely did you make to the app? I'm asking because if you really did simply change the architecture setting, then this is possibly a bug on Apple's side. I'm a Mac and iOS developer, and I'd like to go file a bug report with them if that's really the case.