Welcome to the forum!
Why were you surprised that a backup file that was just saved, has a current timestamp? Or do you mean that a lot of time passed since the crash?
I had a similar experience where the backup file after a crash looked like an older file. But after a lot of panic and investigation, I found it was the same file, but that the layer I had been working on had somehow been hidden. And a layer I had worked on much earlier was visible. When I reset all the layers' visibility, everything was ok.
I'm not sure what "too many heap sections" means. I know in earlier versions of Inkscape, let's say pre 0.48, it was common to see that error message. But since recent versions, I haven't seen it at all....except for once recently, when using the new Gradient Mesh tool, I got the heap sections error again.
I reported it on the mailing list, and I can't remember the specific answer. But I can look it up later, and I'll post again.
Did you mean that you saw that error after you clicked Save? I only remember seeing it during a crash. I don't know if there's any significance to when the message appears.
I wonder if the backup file was saved somewhere that you wouldn't expect? The only thing I can think of, is to try searching for the file. Maybe it did get saved into a different folder, somehow?
I'll post again when I find out more about heap sessions.