How do you activate powers? Is there any way to do this? If I have a power that grants 2 armor for example, and lasts for a long time, how do I activate this so that the armor part of the sidebar on the right reads correctly? Or will I have to remember that it's active? (Which is fine, I just want to know if it's possible)
Powers that have a constant effect will already be implemented as improvements. Anything that requires that you toggle it will not be, so the best way to do that would be to use the Custom Improvements tab to create your own and enable/disable them as necessary. I have a plan to enable doing this directly from the powers tab, but it's a low-priority enhancement.
For equipment: Is there a way to create a category or location for items? If you have a bunch of different types of ammo and want to condense them into a dropdown until you need to look through them, or a bunch of programs for a Decker, is there any way to do this?
You should see an Add Location button on the gear tab. You can drag things into there and collapse them. Programs you can't really have loose because they're treated as plugins.
I had a crash on trying to load a character build - no error message. It happened twice.
Unfortunately those crash messages don't include any content, which I believe is due to a bug that was fixed in recent nightlies. Mind giving the latest build a crack to see if that helps?
Kill Code is in current nightlies; I've stalled the release of a new milestone build to deal with some issues that have cropped up, but I think we might have it licked by the end of the weekend.
For what it is worth, there was a change to the sourcebook options recently. It looks like everything is selected without anyway to remove it. The column on the left where you used to click checkboxes has the checkboxes removed. That is a digression though. 
Enabling and disabling Sourcebooks was moved into the Character and Printing tab.
