So, this is just to let people who see this message for a very long time when updating ISPConfig, wait a little longer. I found a lot of people who had aborted and tried to find the backup and reinstall, and sometimes it can take a while. I waited close to an hour and it finally worked. I ran the "top" command and gzip was going for about 30 min. before it worked. Anyway, thanks to the patient people who led me to believe it would finally go.
I had this issue with Ispconfig2 and it was related to temp files. Temp files where several GB in size. This was long time ago, maybe it's not related but good to know