I am not saying that the following is definitely the issue but it is a possible cause and I suggest you look in to it further.
I have found that often but not always Windows users are prone to accidentally use the wrong file extension for a file - particularly for video files. If hypothetically an MP3 file was given a .mp4 file extension this does not magically convert the file to MP4 format aka AAC but means the file is wrongly named.
As it happens Windows tools seem more forgiving of this type of mistake and Apple or more accurately Mac tools are more rigorous about checking things match properly. Therefore iTunes may see a file with a .mp4 file extension, then look at its contents and see it is not an MP4 file and reject it or in trying to process it get very, very confused. ;)
Similarly at least for video files, I have seen one of the main video 'containers' e.g. MPEG4, AVI, WMV, etc. which can be regarded as just 'envelopes' contain media using a CODEC not normally used with that particular type of container. If again hypothetically a .MP4 file contains instead audio compressed with say the MP3 codec then this would again confuse iTunes which is rigorously obeying the rules whilst other less careful programs might accept it.
Try using a tool like this https://mediaarea.net/en/MediaInfo to give a report on the file. It should list the 'container' format and the codec used. Do this on a working AAC file and a non-working one to compare.