I think there may be a glitch with the replace all functionality as I have had a similar experience.
I have a saved Group (to clean up the .css page) with about 9 entries. I hold CTRL (to prevent it from defaulting to All HTML Files) and click on replace all...and it skips the first entry every time. I have to run it a 2nd time to get it to apply.
I hope that helps someone figure out if/where the glitch may be...