"I see it mostly with QuickBooks Desktop"

For QB, you would be using QB to make backups into a folder that is not the same as where the Company Files (.qbw) and associated files are located. That way, Carbonite, Mozy, etc, only need to mirror the backup files. If you have them mirror these relational database working files, you risk corruption because you get what is called Conflicted Copies. I know Lacerte works similarly. I don't know about ProSeries under-the-hood restrictions.

When a program is open, such as QB or Lacerte or Word or Excel, they may or may not open the data file (the company file, the tax return, the document, the spreadsheet) as "in memory" (this is how Word and Excel work) or as Live Connected. When it is live connected and constantly updated, that's when a mirror routine such as Carbonite and Mozy will freeze, or lock up, or make a system freeze while working; it's Record Locking. It would be like you trying to use a single-slot toaster, but I already put something in it. You have to wait.