What sort of persistent data is generated by bundled Tor?

I recently did an experiment using the Tor Browser Bundle for GNU-Linux. I created two directories, A and B, and placed an identical copy of Tor in each one.

Next I placed a simple python script in directory A that both launched the vidalia package and, when exiting the network, deleted the entire contents of A with the exception of itself and rebuilt the bundle from the original archive.

What surprises me is that after about ten hours of browsing each, A and B now show a distinct difference in startup time. Also curious is that I get a message in the log of B that never shows up in A: new control connection open which is a notice level advisory.

This has nothing to do with what I was originally testing but now I'm interested in what exactly is going on.

By the way I do not have to rely on Tor for my personal safety as many are forced to do so even if you just have a hunch I'd be interested in hearing it.