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Same problem for me. It turns out that the cause of the problem was the new JungleDisk 3.0, which rudely installs three overlays named "1Sync..." "2Sync..." and "3Sync..." pushing the Tortoise ones off the end.
Just delete those JungleDisk keys in the reg hive listed at the top (or prefix them with z_) and re-start the system and Tortoise should work fine again.
Given that this overlay limit exists in Windows and is easily hit with current tools, tool vendors really should ask during advanced installation if the user wants to install them. I have no need nor desire for the new "Sync" feature and don't really care for the tactic of stuffing the icons at the top of the list with clever naming. Shame on JungleDisk.
If you want to use Tortoise from within a 32 bit Application on Windows 7 64 bit, you need to install both the 64bit and the 32bit versions of Tortoise. According to Tortoise's makers, this works fine. (source)
I had same problem here with TortoiseSVN 1.6.16. Icons were fine, but then I installed and uninstalled TortoiseGit and suddenly the TortoiseSVN icons stopped working. Looking at the registry I discovered that uninstalling TortoiseGit also removed all overlay icons. I simply reinstalled TortoiseSVN and it fixed the issue.