Those bonuses are set to be random, for variety. So that starts aren't always the same. You might get lucky with the bonuses, you might not.
You can mod this though, and make Earth always have a Food bonus for example. It's in HomeSystems.xml. The Great Link always has an Energy bonus, due to its lower pop cap.
That's random too. You can actually tweak that too, in Tables\UniverseTables.txt.Also, just did a new game+F12 and hunting for no-hab-planet systems, and unlike that playthrough I spoke of that had three ahandful of sectors from Sol in that game, this one... doesn't have ANY no-habitable-planet-in-systems for both Alpha and Gamma quadrant. ... *vulcan eyebrow*
... haha just started Beta quadrant, and boom, found one... no bonuses though. ...
The current build can still produce the index crash, caused by scanners. Thanks geordie for your great observations!
I've just disabled the AI building them, and uploaded a new patch.
@Iscaran, geordie, anyone else: could you check this new patch to see if your CPU issues get any better please? I made one change that might help.