I'm on an iP5 (6.1.2) and for mobiletimer I agree that you have the name right though, so I'm a little stumped. Do you have the icon the right size? I have had this problem with the mail app (and I think it was with Jaku) and it turned out the icon needed to be Cydia size at 118x120.
This didn't work. I even removed all the icons from that folder and the the original jaku clock icon remained. This has to be the wrong location or something.