Check In failing after upgrade

I recently upgraded to workflow 2013 version 3.0.7.0 and a workflow that has been working since January is now failing.

It is a simple workflow:

1.  Check Out Item

2.  Set Custom Field Value

3.  Check In Item

4.  Set Approval Status to Approved

5.  Set Item Permissions (set all groups to read only)

It is failing on the check in with:

"Error checking in item. The workflow failed because the action requires the document to be checked out."

If I add a wait in between #2 and #3 it succeeds.

I have many other similar workflows, so I'd rather not have to add waits for all of them.

Any ideas?