When in Parallels, if I use a hotkey like Command+Number to run a workflow that activates another app, it does activate the other app but also results in activating the Start Screen (in windows 8, or the Start Menu in Windows 7).
Certainly this is an interaction between two programs. It might be a problem in Parallels versus Alfred v2, however it did behave differently in v1. (I've checked, and I don't have a conflicting Workflow mapped in this case. ;-)