The CTRL+/ are no longer working in build 4621
also the icons are gone (below the indent icons on the left)

check if shortcut is assigned to the function:
Tools->Settings->Editor shortcuts->Add/remove line comments

They were empty. And I could not enter any special combination like CTRL+] or CTRL+/ when I tried to add them again.
All special CTRL combo's were gone in the shortcuts.

But I found the problem. I changed the regional keyboard settings earlier yesterday.
It seems phped has a problem with that if you dont reboot the system. Which is not required or even asked by windows.
(and no phped not running then i changed it)

So it's solved, i rebooted the system today and the sortkeys are all back.

sorry for the confusion.

Probably you tried to enter the shortcuts by pressing those combinations while the keyboard was in non-US layout. In non-US layouts, / and ] are often used for international characters and therefore can't be used as shortcuts in PhpED.
Anyway, you could enter the shortcuts LITERALLY, in other words just enter symbol by symbol c-t-r-l-+-] in the input: