Checkboxes no longer present to stage and unstage files

I upgraded from 1.8.3 to 1.9.5 today. My unstaged files no longer have a checkbox on the left (see screenshot). So it is not easy to add files.

Additionally - if you have a single file. Right click it and 'Add', and then in the staged files area press 'unstage selected'. The file moves back down to unstaged files - but the 'stage selected' button remains greyed out and unclickable. See second screenshot