A huge thank you to @TashasEv for that answer. I was having the same problem for days and couldn't figure it out, but your answer set me on the correct path.
Here's was our problem - whenever a workflow would run, we would get an error saying that the workflow failed to run, and "Workflow canceled by System Account."
As I went deeper into the workflow files themselves, I was seeing that some, but not all of them, were checked out. I tried to check them in. I received the exact same error you did about not being able to check the file in. I checked the ULS log around the time I attempted to check in the file and got this:
SOAP exception: System.Runtime.InteropServices.COMException (0x82000009): You must fill out all required properties before checking in this document.
at Microsoft.SharePoint.SoapServer.ListDataImpl.CheckInFile(String pageUrl, String comment, String CheckinType)
at Microsoft.SharePoint.SoapServer.ListDataValidatorImpl.CheckInFile(String pageUrl, String comment, String CheckinType)
at Microsoft.SharePoint.SoapServer.Lists.CheckInFile(String pageUrl, String comment, String CheckinType)
I then looked at the content types and compared them to see what was different between my site and another site which was working. Sure enough, there's a column called Client which was set to Required in my User Workflow Document content type which should have been set to Optional. I made the switch, was able to check in the workflow files, and my workflows started working.
A note on the User Workflow Document content type. It is a hidden (seriously!??) content type, so you won't see it unless you open SPD, click "All Files" on navigation, then right-click the "Workflows" special folder and click "Properties". From there, you can look in the Content Types section and right-click to edit the User Workflow Document content type. You'll need to go to the individual column's Administration Web Page to set the properties.
PS. I hate SharePoint.