Why does my project take so long to save?

I have a project that currently has 3 maps on it, with few events. I don't have very many resources imported to it either. Yet it takes several seconds to save.

Meanwhile I have another project that has dozens of maps and tons of events and imported resources, yet it saves virtually instantly.

I have the Steam Cloud service disabled as well.

What could be causing the long save times?

Even if Steam Cloud is disabled, go to "Manage Projects" and make sure to do a "Delete from Cloud" on your project.

That is enabled by default with any new project.

Well but I like to make backups on occasion to the cloud. I just don't need cloud support at every single little save I make.

There are several ways I backup the project:

1. Make a ZIP of the project and stuff it on Dropbox.  This way, it silently sends the backup to the cloud, in the background, without slowing down your work

2. Take said ZIP file and copy it to a USB drive. 

I don't use Steam Cloud because I've heard sometimes it makes mistakes and will gladly restore an older copy of your project and overwrite your newer, current version of the project.  And I don't like the lag when saving, either.  I've seen it take as long as a minute to save a decent sized RPG.

I completely disable steam cloud as detailed above, and I have my main project on onedrive. I work on the project and also save backups locally on whichever computer I'm on to be safe. This makes it so that whatever computer I'm on, the project files have been updated properly, and I have local folders as backup for safety.