Initially I set this up under my own account. I created two flows which we identical with the exception of the Subject Line and the output folder. Essentially I want to send files with different subject lines to the appropriate folder. This worked just fine.
I then created a general account (obviously I do not want to use my own). I set the workflow up just the same but now it often gets the Skipped status - about 75% of the time.
I then changed the process for testing... I created two folders in the O365 Outlook Account and created a rule based off the subject line to move email to those folders (working just fine). I then updated the Flow by removing the Subject Filter and changing the Folder from Inbox to (in this case) to PaymentProcessor folder
I just removed the Subject Line and now I am using the Email Account (rule) with the subject line to send the inbox mail to a folder and have the Flow look there - still get the Skipped status
The Output is the same regardless of the configuration...