I had the same error and couldn't get around it except to start with a fresh slate and reinstall over 50Mb of apps and data. Somewhat like you, I had only gotten Hotsync to work well enough to install some files that couldn't be installed via the GVM launcher. (As far as I am aware, the launcher will only install .prc and .pdb files).

So, I spent hours getting Hotsync to work well enough to backup the data to my PC. Hotsync crashed, crashed and crashed. The prob turned out to be that Hotsync was choking on specific files (see another thread about this). I was able to find those files one by one and flip the backup bit on those files off until I got a smooth backup.

I created a new store, loaded all the apps on it and nearly had it done before the GVM trashed the store. I started over again and had more luck. My advice to anyone who's building a large store is that they should do checkpoint backups through the process in case the GVM sends the new installation into the black hole.

I hate to think how long this took me, but I think it'll be worth it. Exit times are much, much faster. That may not seem like much to those who have smaller stores; however, I know that some of my catastrophic failures have occurred when the GVM crashed while exiting. It only makes sense that if the GVM is writing a lot of data back during exit that a crash there might leave inconsistent data. We'll see how it goes. I think I'll see fewer crashes and less data loss.