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Maurice, Which device and OS are you testing this on, I assume a TC55 with a GMS build?
I suspect that when starting the app from the homescreen, a different Activity ClassName is used.
Thanks for your answer. This is on a TC75 (Android 4.4.3), but the issue is now fixed.
The problem was that I had left Datawedge open with that profile in edition. I realized that was the problem when I noticed the scanning no longer worked in Chrome either. After exiting out of the profile properties I'm now able to scan both in Chrome proper and in the Web App launched from the Android Homescreen.