I am not the expert on BiblioSpec, but I don't think modifications are supposed to look like that, with the square brackets appearing before the first amino acid in the sequence. With N-terminal modifications, my understanding was that they were supposed to look to Skyline as if they were attached to the first amino acid, so the square brackets are supposed to go after the first amino acid.
There might be a bug in terms of what BlibBuild.exe is putting into the .blib file when you are building the spectral library from your DIA-NN results.
Can you send us your .speclib file? If that file is less than 50MB you can attach it to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick