Lenders are running things (this is BK, after all) and they had a deadline when something (leases, as near as I can tell) had to be resolved for certain stores, some of which are very profitable for the chain. The deadline was going to trigger an auction and store closures, which probably no one wanted to happen. It looks like this was a negotiating ploy with the people leasing the space to the chain.
I always find the game of chicken involved in bankruptcy -- and the lead up to bankruptcy -- somewhat amazing. I keep thinking that if someone comes to you and says, yeah, you know, things changed and I can't pay that any more but I could pay this -- and you _know_ you can't get any better than the new deal on the open market -- shouldn't you take it? Isn't that the rational thing to do? The Borders example seems fairly minor compared to the nonsense going on in housing, but still.