I've seen this bug for as long as I can remember, and yet it's consistently ignored and people are told it's been solved, yet still I see it in the latest release (2.0.4).

For some reason, no matter what force you specify in part.cfg, mechjeb's auto-staging forces it to a minimal, if not nonexistent value. This causes parts being separated to remain next to the rest of the craft, with no clearances. Any angular motion causes collisions that tend to cause catastrophic failure. Even without angular motion, accelerating away from decoupled parts can still cause collisions.

Craft: http://pastebin.com/sacDfV6B
KSP: 0.19.1.54
Mods: Clean install + mechjeb 2.0.4

Reproduction:

Load craft, enter assent autopilot, enable auto-staging, launch.

Observe: the tanks fall off with no separation other than that of the decoupler part itself.

Load craft, enter assent autoppilot, DO NOT enable auto-staging, launch.

When external tanks empty, preform manual staging.

Observe: tanks are pushed away from craft, causing a noticeable spin in this craft due to force not being directly applied to CoM of tanks.

Behavior applies no matter what parts.cfg has listed.
Behavior becomes much more obvious with higher force values.

Yes, it wasn't the staging that was happening too fast, something isn't working properly with the current way of staging things. I'll find it, and I'll fix it this time for good.

Can't wait to see this working in the next update. I'd test it sooner if I knew how.