Why don't Registry edits "stick"?

[msh441]

OK, I've recently "upgraded" to Verizon's 6.5/Sense 2.1 and I'm running into a reoccurring problem that I did not experience running 6.1/TouchFlo3D.

There are a TON of mods and regisry edits that just don't seem to stick when powering down, or soft resetting the device. I've particularly noticed this with notification light tweeks, memory edits (Dynamic Resourse Proxy edit), Opera edits (casche and tabs edits), and while trying to delete HTC start menu items etc.

I'm using Resco's File Explorer and Registry Editor and I'm fairly comfortable navigating and tweeking registry items or .xml file.

So what do I have to kill to get my phone to retain my work and behave how I want it to?

Please help!