You have run afoul of a quirk of Excel's calculation options - the setting is saved at Workbook level, but applies to Excel at Application level. You can see a more in-depth explanation in Expert Skills Session 3: Advanced Functions (Lesson 3-17: Understand calculation options (manual and automatic)).
In a nutshell, Excel's calculation mode is set that that of the last workbook that was opened and affects all open workbooks. This means that if you open a workbook that was saved with Manual calculation mode, all open workbooks will be set to Manual calculation. If you then open a workbook set to Automatic, all open workbooks will use Automatic mode.
To make matters worse, if you save any of your open workbooks they will be saved with the current calculation mode, so you can very easily get tied up in knots and start to think that the calculation mode is changing at random.
In your case it sounds like you have one or two workbooks in particular that have been saved with Manual mode and they are the cause of the mode switching when you open them. If you can locate these workbooks and re-save them with Automatic calculation mode you should find that the problem disappears.
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