I have no interest in fine-tuning the taskbar transparency, particularly with regard to some other third-party software. From your post it is evident that Aero Glass keeps changing (used to support the taskbar, now doesn't), which makes it particularly difficult to be compatible with it.

What I can promise is this:
1) If you check the "Disable taskbar transparency" setting, the taskbar will be opaque on a stock unmodified Windows 7, 8 or 8.1
2) If you uncheck the "Disable taskbar transparency" setting, Classic Shell will not touch the taskbar, which will allow any other software to have its way with it
3) If you check the "Enable Aero Glass" setting, the start menu will be drawn as it is on Windows 7, allowing any software that tries to emulate Windows 7 aero effect to do its work

The fact that a combination of "Disable taskbar transparency" and Aero Glass gives you somewhat desirable effect is purely coincidental. Neither me or the Aero Glass developers can guarantee that this will continue to function in the future.