How would a project completion mode switch from automatic to manual?

In my experience, people tinkering with settings they don't understand would be the only culprit. I have never seen project settings change by themselves. 

Are they adding a second subtemplate to any of these projects? This shouldn't change that particular setting but it's worth looking into.

The one place I know I've seen that happen is if the user opens a blank project and then later attaches the template. That setting does not get updated in that instance. I believe the same would be true if Fusion performed the same action during conversion to a project as well.

If you're truly visiting a project after it's completely setup and it's correct then but changes later, I'd suggest a Report-Report with these three columns. What it produces will be horribly ugly and unreadable, but searchable. If you then filter on 'completionType', it will show you any reports where someone may have mistakenly pulled that into a view thinking its meant to do something entirely different. New folks building reporting can cause all kinds of weird chaos.

I'd suggest turning on tracking for the Completion Type field in the Update Feed and then building a JE report to isolate what's causing it also.  

Just for some added info, Here is what changes when a template is added to a project:

• Project Name does not change
• Custom Forms
  • Will add forms if not already present
• Overview
  • Description – will add if blank, will not overwrite
  • Basic Information
    • Status – will not change
    • Priority – will not change
    • URL – will add if blank, will not overwrite
  • Project Condition
    • Condition Type - will not change
  • Project Dates
    • Schedule Mode – will not change
    • Planned start date – will not change
  • Project Association
    • Portfolio – will add if blank, will not overwrite
    • Program – will add if blank, will not overwrite
    • Group – will add if blank, will not overwrite
    • Company – will add if blank, will not overwrite
  • Project Stakeholders
    • Owner - will add if blank, will not overwrite
    • Sponsor - will add if blank, will not overwrite
    • Resource Manager – adds cumulatively
  • Finance
    • Budget - adds info if blank, will not replace
    • Performance Metrics – will change, budget info (above) changes based on these settings
    • Benefit - will add if blank, will not overwrite
    • Cost - will add if blank, will not overwrite
    • Revenue - will add if blank, will not overwrite
  • Project Settings
    • Milestone path - will add if blank, will not overwrite
    • Completion mode, summary completion mode, update type, schedule, user time off, resource leveling, risk, do not change
    • Resource Pools – add cumulatively
  • Task Settings
    • Task Default Custom Forms – will not change
  • Access – all settings change