OK to clear things up, let’s forget the word ‘edited’, and just say ‘looking’ at the wrong file.
Andy is right in post no.2 when he says it should change, although you hadn’t told us you were running Reboot until afterwards, which makes all the difference when speculating.
Actually yes you are right, we should have this ‘tied up’, but Reboot is a relatively young theme in that it was only released in the early part of the year, and without feedback on these issues some of them are not always easy to spot. In fact this issue by the look of things has not only been present for quite some time, but never reported by any other members up until now!
Having looked into the subscriptions and watches .spcss files I can see that actually they do specify a hex number for the unread count, whereas for some reason PM’s don’t. It should really be all one way or the other, so I will make sure that the next update to Reboot includes a fix to change the colour of the unread PM count to red.
Hopefully we will have the next update out within the next week or so, so depending on what you want to do – you can either wait for the fix, or edit the .spcss file. If you do choose to edit the file then there would be no need to make a child theme as the update will include the fix.