Thanks for your input, Frobozz.
The Audio CRC is identical. I think it would have to be, given that the wav files are identical after converting from FLAC to wav. I checked with the FC command in Command Prompt.
I do not think Windows Media Player Legacy has been involved here. At least, there is no change in the metadata for the file, the date/time for "last edited" is identical for both the original and the copy.
Here is an intereseting bit: All data in Analyze Audio is identical, with the exception of Bitrate. This is slightly higher for the bigger file (the copy). At first I thought this was because bitrate was calculated by file size divided by duration. However, after testing, I see this is not correct. Changing the embedded cover art to a bigger file makes the FLAC file bigger, but it does not change the bitrate in Analyze Audio.
Could extra padding somehow have been added?