I had something very similar happen once when I used Registry Mechanic. I lost a few of my System tools and some of my Administrative tool links. Crap Cleaner broke my dual boot. I had to create my own shortcuts and reinstall my second OS. Since then I've sworn off registry and system cleaners. I've heard that some garbage in the registry hurts nothing at all and Disk Cleanup takes care of cleaning. I use no third party maintenance tools at all.
Operating System Windows 7 Ultimate x64
Computer Type Laptop
CPU Type and Speed Intel Core i5 430m dualcore
Motherboard Chipset Inspiron 1764 Intel HM55 Chipset
System Memory Type 4 GB DDR3-1066 SDRAM
Video Card Type and Speed Intel Graphics Media Accelerator HD HDMI
Computer Monitor 17.3" HD Laptop monitor
Hard Drive 3B29 WDC WD5000BEVT-75ZAT0 ATA 465 GB IDE
Optical Drives Optiarc DVD+-RW AD-7585H ATA
Network Adapter Realtek PCIe FE Family Network Controller + Dell 1520 Wireless-N Mini-Card
Anti-virus Software ESET Smart Security v4
Computer Skill Level Self-Taught Expert