That's at least strange. Never seen something like this before, the only thing I can advice is to try newest version of startorb changer [link] or roll back and try 2.6 version of it, which I was using and everything displayed right.
Thanks, to change icons on taskbar you should firstly create shortcut for application (which you want pin to taskbar) than alt+enter on it for properties and in "shortcut" choose "Change Icon..." than select any "*.ico" icon you want. After it changed simply drag&drop your shortcut to the windows taskbar to pin it.
2nd option is firstly pin all programs you need to windows taskbar and then go to "C:\Users\[User name]\AppData\Roaming\Microsoft\Internet Explorer\Quick Launch\User Pinned\TaskBar" and then change icons individually for each app from there.
3rd is to use use automatic icon changer application like 7conifier for example - [link]
Thanks dude, yeah I noticed that odd flash light on mouse over recently, before I didn't use any windows special effects on windows except transparency and content while dragging, so that's why I didn't know about this before. As for alpha channel, for some reasons it didn't work with 1 pixel width text properly.
by lining up I meant that different themes has different taskbar height. You must pick that one, which perfectly match your taskbar. I don't know why it's broken for you, I'm changing start's orbs with "Start Button Changer v 2.6" so you may try it as well, btw run it as administrator.