System tray icons keeps disappearing 64bit desktop

Hello, I've run into a strange issue, the system tray icons keep disappearing (volume, wifi, action center). It usually happens after I restart the computer, but not all the time.
I'm running windows 7 home premium 64bit with a nvidia graphics card, and intel i7 3.4ghz; on a desktop computer. I'm also using a custom windows theme, but I've never had issues.

Last actions before issues appeared:
Note: I recently had an issue where explorer kept crashing at startup, I tried to run system restore, but the restore failed and said something about not being able to extract something like system root/[what ever]. Somehow explorer stopped crashing without me doing anything. I'm telling you this just in case it may help you find out what's wrong

Thing's I've tried:
-running the fixit from microsoft
-checking the settings in system tray icons (all are greyed out except clock)
-restarting explorer.exe

Any help would be appreciated.

Okay, I tried step two, the network and the volume icon are enabled again, but the action center is still greyed out

Yes, I'm able to open Action Center from the control panel.

Yeah I restarted the computer, I also restarted it after using the updated REG files but it's still disabled


EDIT: Even after restarting the computer, I had to manually restart the explorer process and the network and volume icon appeared, I looked for the action center icon and it was still missing and grayed out.

Then, after few minutes i moused over the tray area and the action center icon appeared out of no where.
Can you explain to me why this happens? I've had this issue before, but never this severe, I've always noticed that Windows has the strangest glitches in the simplest tasks.

Thanks for taking your time to help me

Okay, I'll scan it over the night and let you know the results, and once again the icons disappeared after restarting the PC...