You could argue that this is by design, but ... It looks to me like when you remove all tags from a FLAC file using the "Remove Tag" button, the complete Vorbis Comment metadata block is replaced with padding. This removes the vendor string tag which contains the version of FLAC used to encode the file. The value then gets overwritten later when you re-tag, but the data may not represent the version used to code the file (it's pure luck what you get, depending on wht you use for tagging).
I think it would be better to retain the vendor tag, even on a remove tag operation, as (I think ), it's supposed to reflect the version used for encoding the file ...
Minor issue, but thought you should be aware.