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Strange repeated permission popup

Every now and then (though it's becoming more frequent), "shell has been granted Superuser permissions" will pop up repeatedly at the bottom of my screen. It won't stop until I power off the phone. Started out maybe a month ago, did it once, then once the next week, and, in the last two weeks or so, has started doing it multiple (more than 2) times a week. Today, I have had it happen 3 times already, once right at boot.
Anybody have any idea what's going on and how to fix it?

XT912 running ICS 4.04, rooted, slightly modded (I changed the font), CWM bootstrap with the "start-at-boot" .zip applied, and the hotspot SQLite hack.

P.S.: Cannot screenshot anything right now, coffee spilled on phone and volume rocker not behaving.

P.P.S.: Anybody know how to remove the CWM "start-at-boot" or is it permanent?
 
Google CWM onboot remove droid razr and you will find the zip to remove it, don't want to link to another site.

Not sure what shell is asking permission for, how did you change the font maybe it has something to do with that?
 
I know it isn't a fix for why it is constantly using super user access, but have you tried turning super user notifications off so that it stops popping up all the time?
 
I understand not linking to another site.

As for the font change, I used Rom Toolbox Pro. I have never had an issue with it before and I have changed fonts a couple of times. It didn't seem to correspond with a font change, since my last font change (before last night) was well over a month ago and the issue randomly popped up some time after that, but the fact that RTP just changed the font interface... it could very well be what caused the increase in appearance (if it caused the issue in the first place).

Just to cover all my bases here, any other ideas of what could cause the repeated permission dialogue?

I may try a factory data reset and see if that stops it (leaving the font alone), if I can't figure it out any other way.
I'd really like to figure out if it is RTP, so I can email jRummy with the issue.
 
I keep my permission notifications on so that I know when something is accessing root. I play around with my phone a lot, and every now and then I end up with things accessing root that shouldn't. Can't give an example right now, off the top of my head, but it has happened on my droid 2. That being said, it's not a bad idea if I can't figure it out.
 
Addendum to my original assessment of the issue. I have had a few more instances of the repeated popup, and have noticed something else. Every time the permission notice pops up my screen jumps slightly. I am unsure if the jump is caused by whatever is requesting the permission, or if the popup is the phone fixing the jump. Anybody?
 
Okay, so I have had to actually reflash .211 and did two FDRs. I was removing bootstrap for safestrap, which I like better. The popup has ceased, but I am still unsure what caused it in the first place.
 
Same problem need help

I have the droid razr m and have it rooted. It has happened before but for example this morning I woke up and turned on the screen and it started popping up with the "shell granted super user access" pop up. I looked at the log and it said it did it over 100 times in 2 seconds. I don't know whats causing it or how to make it stop. I want the shell to stop accessing super user not just stop the pop ups. I notice when it happens anything I am doing slows down or skips especially if I am listening to music. Any ideas guys?
 
I ended up doing an FDR because of other issues, and that fixed it. Haven't seen it since. But that doesn't address what caused the issue.
 
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