It can't be a read-only issue if the image tag initially shows the correct information. i.e. The image is in the file.
The default note symbol appearing is likely a thumbnailing issue, not a Cover Art issue. But that could be caused by the Cover Art in the media files being changed by something else. Maybe Auto Import is checking the file, finds a change, updates the Library, and can't find the correct Cover Art, as indicated by the <cannot load image from file> message. If DBPoweramp or some other software used for tagging is running, it may be updating the file.
Why would that happen? If the FLAC file has more than one image file in it, as indicated by the <various internal images> or <various external images> messages, MC may not handle that correctly. Others have suggested this. You would hope that MC just used the first image it found in the file, but experience would suggest that doesn't work too well. If this is happening to specific files, open a example with a tagging application that can see multiple image tags, remove the incorrect ones, and see if that fixes the issue.
If the problem exists for files where both an internal Cover Art image is stored in the file, and there is an external Cover Art file, delete the external image and see if the problem goes away. MC may not be handling two sources of Cover Art well.
When you see this happen, refresh the Views and see if it corrects itself. If it is a transient problem, that points to files being updated by something. Or possibly thumbnailing stumbling.
So, if I have the Tag sidebar open while clicking through the tracks the art will show up. However, the art for the album itself will not.
This would indicate that the thumbnail still exists in the thumbnail database, but the Cover Art no longer exists.
This is also evident in JRemote or when playing locally in MC where the album art shows the default quaver symbol, but when the tracks start playing the album art is shown.
I'm not familiar with JRemote, but I don't think it uses the MC thumbnail database at all, rather it uses the internal image tag in the file. If you mean that you use JRemote to play to the MC installation, then JRemote can't find the internal image tag so shows the quaver, but when you play to MC it can find its thumbnail or the real Cover Art image, and displays that.
Does that give you some more things to check?