XSitePro backs up all the files in the XSitePro Data directory 'My Documents/XSitePro-Data/Database'
We did have an issue with a year or so with XSitePro creating too many files here.
So my next suggestion is that you make sure that you are on the latest version of XSitePro.
You can find the update to XSitePro v2.530 here:
http://licensing.intellimon.com/xsitepro/downloads/xsitepro2-update530.exe

If you are on the latest version of XSitePro. the next suggestion will be to re-build the XSitePro database:
1: Please export all your websites to XSE files.
2: Quit our of XSitePro.
3: Rename the XSitePro data folder 'My Documents/XSitePro-Data/Database' to 'My Documents/XSitePro-Data/Database-old' .
4: Restart XSitePro. This will cause XSitePro to create a new database folder.
5: Re-import all the XSE files. This will make sure that only the real website data is there to be backed up. :)

If the backups still take an age after this, you will need to check the size of any audio and video files in your websites.
It could be that the website size is slowing down operations.
If this is the case, raise a support ticket as I have some suggestions that will help. :)