Why does a missing label 11plex TMT shows up at almost 50% intensity compared to other labels?
The developers answered along these lines:
This might be a normalization artefact. Reporter is normalizing the ratios so that the median is 1. So, if the label is almost not present the noise gets increased. To check that you can turn of the normalization. This function is currently not documented. The developers are working on it though. 

GitHub issue