The issue you are referring to is something that we are aware of and are working hard towards a resolution, however, we do not have a timeframe for this to be completed as yet.
In the meantime you can send a custom workout by changing your Connect to Classic View. To change the view please follow the below path:
Select the head and shoulders icon from the menu situated on the left hand side of the web page
Here select Switch to Classic Temporarily
To those of you who have a license of the Fit File Repair Tool: since version 6 the tool includes a Workout Editor. It allows you to define workouts and export them into workout fit files which you can copy to your device afterwords.
Defining steps with a duration of less than 1 minute is possible, I just checked it.
To activate the Workout Editor (it's a hidden feature of the Repair Tool) go to Settings -> Program Settings -> Activate Workout Editor.
You can download a screenshot of the Workout Editor here: https://dl.dropboxusercontent.com/u/91455145/workoutEditor.jpg
Best regards
Mathias