I appreciate you offering that clarification, hlxanthus. What happens for me is this: when I boot the phone from powered off, it boots Android, opens the Home screen, and loads the SD card. A few seconds later, the radio signal and WiFi icons turn on, and my Home screen apps appear. After that, nothing happens. I can't get any apps to load, can't open the app drawer, can't open apps in the dock. One time, I specifically waited to see if it would go away automatically and it didn't. It only starts responding after a long press the home button.
I clean installed the ROM again and I don't have that problem. I did two things to modify the ROM after installing:
1. I used NoBloat to uninstall some stock apps and the HTC keyboard. Perhaps uninstalling the HTC keyboard baked in broke the files somehow. I've always used NoBloat to uninstall apps I don't use, and I haven't seen stability issues.
2. I messed around with the No Frills CPU app settings. You mentioned that the low clock speeds can cause the wake issues. Well, after a clean install, I didn't touch the settings, and I don't have wake issues anymore.
Does deleting apps like Latitude and Search break the system? Thanks.
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