Thanks for you response.
I suspected Excel's load time was to blame but the wording in the config seemed to offer a solution. Especially as I only had one application in that action.
I'm something of a novice with workflows, admittedly. Perhaps it may be worth updating the config dialog box or the help page (http://support.alfredapp.com/workflows:config:actions-launch-apps-files) to include your above response?
A little more clarity might help others trying to get to grips with this functionality.
In the meantime I'll look into 'delay' in applescript.
Thanks again.