Well, like I said, deselecting Quicktime decoder solved it.
A quick look in the log shows tons of things like this:
2013-06-11 00:00:19 Decoder hang up on file: U:\MP3\Ripped CDs\Glass, Philip\Philip Glass - 1973-5 - CD.jpg, decoder: Apple QuickTime Framework
2013-06-11 00:00:19 System error [2]: The system cannot find the file specified.
2013-06-11 00:00:19 CProcessLink::InnerSend:174 failed [-100]
Note that I DO NOT have image comparison selected in Settings, but this explains the decoder problem, and also explains why I see decoders when running from the cache, as these files haven't been "cached", so the program will try to decode them every time and fail!!!
Despite the above I'm still having problems getting a complete scan with the latest version.I get continual crashes which seem to be out of memory. I have 4GB on a 32-bit machine, but some error causes the Similarity.exe to swell to 1.7+ GB.
Now I've solved the decoder problem, I'll start to see what can be done to solve the other problem.