You didn't see them because they were now there
I had probably selected the file and forgotten the "Add" button.
Actually the -fixed file is the one starting with $FF $FF $00 $00 $00 $00.
I did that as hack to ensure it is recognized as ROM, because that is clealy not a valid EXE header.
The hint with SHIFT shows that the studio find tons of warnings/error when import the plain (-wrong) ROM.
Yet it considers it a valid EXE at the end.
[Image Database Manager] Initialized, 1245 image signatures loaded.
[USB Manager] Initialized and running.
[Image Converter] Valid Atari EXE file, imported 7052 bytes from ATARIMAX ROM-001-WRONG.ROM => Not correct, is no EXE
[Image Converter] Imported 8192 bytes from ATARIMAX ROM-001-FIXED.ROM => Correct
[Image Converter] Examining segments in C:\Users\JAC\Desktop\Atarimax ROM-001-wrong.rom
[Image Converter] Invalid segment [0xA0A9 - 0x852C] at 0x00000000 -- assuming zero length.
[Image Converter] Segment [0x8500 - 0xA981] at 0x00000004 extends past end of file.
[Image Converter] Segment discarded, treating as zero length.
[Image Converter] Valid segment [0x8506 - 0xA083] at 0x00000008
[Image Converter] Valid segment [0x0000 - 0x0000] at 0x00001B8A
/CUT MANY MORE OF THESE ERRORS/
[Image Converter] Valid segment [0x0000 - 0x0000] at 0x00001FF9
[Image Converter] Ignorning junk segment. (transfer padding)
[Image Converter] Ignoring 2 bytes of extra data at end of file.
[Image Converter] Warning: executable sets no RUN or INIT address! Injecting RUN address of 0x8506.
[Image Converter] Process completed with 229 warnings and 1 errors.
[Image Converter] Content MD5 is [af3a0e9ad5c786619299bceb84b77a2b]
[Image Converter] Valid Atari EXE file, imported 7052 bytes from ATARIMAX ROM-001-WRONG.ROM