It's rooted and modded yet it updated the OS? Are you running a custom ROM or running the original ROM? On my HTC One which I run GooglePE it updated and I had to root it again to gain some lost functionality that relies on root. It may be worth trying to root the device again first to see if it's your problem but usually opening a SU app will give you a warning that you don't have root.
Only thing I can suggest is you look at /system/etc/init.d/ The scripts in here will be run when the phone boots but seems strange that this is a problem if you are running a custom ROM.
How do you find your HTC One? I've had mine for a while now and it's brilliant, I think it better suits the wife though now the new HTC One has been released.



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