From your description it sounds like you are using the 'Logout User Profile' setting under EM on the phone - but I'm pretty sure this disappeared in 6.x?
Typically you would configure:
1) Normal/logged out settings on the EM phone - including your custom softkey set etc.
2) In your EM dev profile, a setting of for the Softkey Template should leave the standard (phone config) one in place, but a configured one should override the phone one at login.
Only other suggestion I can make is when you make such a change (apply softkey template to the dev profile) you should log out the user and log in again, rather than just reset the phone.
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