After updating Flash with Shavlik, a Nessus scan told me that a bunch of Windows 7 machines still needed an update for the 64-bit plugin version of Flash while Shavlik said they were up to date. Looking at C:\Windows\system32\Macromed\flash on these machines, I see
FlashUtil64_12_0_0_43_Plugin.exe
NPSWF64_12_0_0_43.dll
On machines not flagged, I see 12_0_0_44, and I see this version in C:\Windows\syswow64\Macromed\flash on all machines. Both the 32-bit and 64-bit versions come from the same installer, so I suspect the installer did something strange, not Shavlik. Perhaps some logic error triggered if Firefox was running when the patch was applied. Roughly one third of our Windows 7 machines did this.
We have no 64-bit plugin-based browsers installed, so I just deleted the two old files on the affected machines. It will be interesting to see what happens the next time flash is updated.