One simple step you could take is to install SP08 and see if the issue persists. Even if it does, I'd say you're better off having those hundreds of bug fixes.
I haven't used App Builder either, so I don't know what it does, or can be configured to do, during a save.
It's also possible this isn't an App Builder issue at all. It could be some kind of environment issue. Is a network involved in any way, e.g. saving the file to a remote share? That location could be the problem. Or maybe the location on the disk where App Builder is writing something other than the source (r-code? logs? temp files?) is problematic. If the clusters involved are failing, the disk might have to retry several times to get a successful write. In that case, relocating the files might help.
It could be a problem with your OS. I recall we had significant performance problems in our OE application when we first went to Windows 7. I tracked it down to a feature called offline files which was enabled by default. It wasted a lot of time trying to search a file cache which was actually empty. I disabled the feature and performance returned to normal. I found that problem with
Process Monitor. You may want to run that during a problematic file save and see where the time is spent. In particular, see if there are any two operations where the time delta (which can be added as a separate column) is particularly large.