Do you have that original CUE file, and can you share it?
I checked and there a variety of CUE files that do this.
"This" = overwrite only the library tags of the last track. My theory is that all CUE files always overwrite only the libray tags of the last track, and there is usually no "problem" because the "Title" in the CUE file is normally the same info as the "Album" tag in the FLAC file, and so forth.
Here is one of those amateur CUE software generated files - the information is taken from the filepath structure in an incorrect way. In order to reduce the volume of this problem, I deleted most of these generated CUE files, but I missed this one:
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
TITLE "CD 1"
FILE "01 Vollenweider, Andreas - Behind the Gardens - Behind the Wall - Under the Tree.flac" WAVE
TRACK 01 AUDIO
TITLE "01 Vollenweider, Andreas - Behind the Gardens - Behind the Wall - Under the Tree.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "02 Vollenweider, Andreas - Pyramid - In the Wood - In the Bright Light.flac" WAVE
TRACK 02 AUDIO
TITLE "02 Vollenweider, Andreas - Pyramid - In the Wood - In the Bright Light.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "03 Vollenweider, Andreas - Micro-Macro.flac" WAVE
TRACK 03 AUDIO
TITLE "03 Vollenweider, Andreas - Micro-Macro.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "04 Vollenweider, Andreas - Skin And Skin.flac" WAVE
TRACK 04 AUDIO
TITLE "04 Vollenweider, Andreas - Skin And Skin.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "05 Vollenweider, Andreas - Moonlight, Wrapped Around Us.flac" WAVE
TRACK 05 AUDIO
TITLE "05 Vollenweider, Andreas - Moonlight, Wrapped Around Us.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "06 Vollenweider, Andreas - Lion And Sheep.flac" WAVE
TRACK 06 AUDIO
TITLE "06 Vollenweider, Andreas - Lion And Sheep.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "07 Vollenweider, Andreas - Sunday-.flac" WAVE
TRACK 07 AUDIO
TITLE "07 Vollenweider, Andreas - Sunday-.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "08 Vollenweider, Andreas - -Afternoon.flac" WAVE
TRACK 08 AUDIO
TITLE "08 Vollenweider, Andreas - -Afternoon.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "09 Vollenweider, Andreas - Hands And Clouds.flac" WAVE
TRACK 09 AUDIO
TITLE "09 Vollenweider, Andreas - Hands And Clouds.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "10 Vollenweider, Andreas - Caverna Magica.flac" WAVE
TRACK 10 AUDIO
TITLE "10 Vollenweider, Andreas - Caverna Magica.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "11 Vollenweider, Andreas - Mandragora.flac" WAVE
TRACK 11 AUDIO
TITLE "11 Vollenweider, Andreas - Mandragora.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "12 Vollenweider, Andreas - Lunar Pond.flac" WAVE
TRACK 12 AUDIO
TITLE "12 Vollenweider, Andreas - Lunar Pond.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "13 Vollenweider, Andreas - Schajah Saretosh.flac" WAVE
TRACK 13 AUDIO
TITLE "13 Vollenweider, Andreas - Schajah Saretosh.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "14 Vollenweider, Andreas - Sena Stanjena.flac" WAVE
TRACK 14 AUDIO
TITLE "14 Vollenweider, Andreas - Sena Stanjena.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "15 Vollenweider, Andreas - Belladonna.flac" WAVE
TRACK 15 AUDIO
TITLE "15 Vollenweider, Andreas - Belladonna.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "16 Vollenweider, Andreas - Angóh!.flac" WAVE
TRACK 16 AUDIO
TITLE "16 Vollenweider, Andreas - Angóh!.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "17 Vollenweider, Andreas - Huiziopochtli.flac" WAVE
TRACK 17 AUDIO
TITLE "17 Vollenweider, Andreas - Huiziopochtli.flac"
PERFORMER "ANDREAS VOLLENWEIDER - THE TRILOGY 2CD [flac-8]"
INDEX 01 00:00:00
FILE "18 Vollenweider, Andreas - Con Chiglia.flac" WAVE
TRACK 18 AUDIO
TITLE "18 Vollenweider, Andreas - Con Chiglia.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "19 Vollenweider, Andreas - Geastrum Coronatum.flac" WAVE
TRACK 19 AUDIO
TITLE "19 Vollenweider, Andreas - Geastrum Coronatum.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00
FILE "20 Vollenweider, Andreas - La Paix Verde.flac" WAVE
TRACK 20 AUDIO
TITLE "20 Vollenweider, Andreas - La Paix Verde.flac"
PERFORMER "Andreas Vollenweider - The Trilogy [FLAC]"
INDEX 01 00:00:00