The file list on the commit screen has Modified, Removed and Added files checked as default. If you change the original selection and click refresh, the default files are checked again, losing the selection changes.
Screen shot shows the default file selection at the top, modified file selection in the middle, I then added a new file into the directory structure so clicked refresh, and the bottom shows the defaulted list with the new file.
I have just upgraded from 2.3.2, and this didn't not happen in that version.
(Just noticed the new "Amend" feature which also has it's own default set of checked files... I guess this bug has been introduced with the new feature)