Error: Unable to parse YAML file

After changing the editor serialization to "Force Text" every time I start Unity this error shows up once: "Unable to parse YAML file: [mapping values are not allowed in this context] at line 1"
This error can lead to broken scenes: e.g. misaligned transform positions or broken Font/Sprite atlases but it only occurs very randomly.
We are currently using Unity Version 5.1.1p2 but I also tried with other versions (5.1.3p3 and 5.2.0f3) with the same result.
We tried deleting the library so that Unity will show the exact YAML errors after restart but apparently there aren't any.
We also went through all serialized YAML files with a custom script to check for invald YAML code but everything seems fine.
We even tried deleting all scene files but the error still shows up. Changing the serialization back to "Mixed" doesn't help either.

So how can we fix this problem?

 

Same error on 4.6x versions of Unity never knew what it all meant