Jalview's annotation file doesn't restore annotations added via T-Coffee score properly

To reproduce:
  1 - run Jalview
  2 - load alignment from file 'tcoffee.fasta_aln'
  3 - load tcoffee annotations from file 'tcoffe.score_ascii'
  4 - export all annotations as Jalview annotation
  5 - start new instance of Jalview
  6 - load alignment from file 'tcoffee.fasta_aln'
  7 - then load annotations file exported in step 4

Observations:
Although the t-coffee per sequence annotations are restored, they set to visible and the t-coffee colour scheme is not applied to the alignment.