CE - Model Annotation Not Holding Annotation Scale

Normally, the way I work is to set up a Model Annotation and then use 'stfannotate apply physlabels' and 'stfannotate delete physlabels' to turn the labels on and off as I need them. Usually work great, but when I do it to a file in CE it seems to lose the link to the Annotation Scale for the model and change back to very small text. If I delete the Model Annotation and reapply it still doesn't recognise the Annotation Scale. I can pick a higher Annotation Scale and the text will become usable again, but as soon as I delete and then apply the physlabels, it loses the link to the Annotation Scale.