Initially I was going to suggest that there may be another application loaded and had the scanner locked from being used. But then you mentioned that you need a few reboots to clear things out. Check to see what apps may be loaded at startup. Otherwise it sounds like a possible hardware problem (unless you say it happens on multiple devices).
Also the latest version of EMDK For Android is 6.0 - be sure to run the device update APK that comes with the installation in order to update the EMDK service on the device.
I'm trying out EMDK version 6.0 for Android to see if this makes a difference. Thanks for the tip!