thomas: Describe exactly what you see happening. Can you issue "site crashnow" and does it work? If you try to connect to the server immediately after you see it acting wierd do you at least get as far as the login prompt, an accepted connection, or does the connection just time out? And describe your hardware. I don't think you have a hardware problem, but I was able to see this bug on multi-processors in the past more often so that's useful to know...
Microsoft offers a tool called app-verifier. It's freeware. Try downloading that and setting it up to monitor ioFTPD. It will make ioFTPD use a lot of memory and be a bit slower but it can catch a lot of issues. If it finds any let me know. There are 1-2 false positives, but for the most part if it complains it's something that needs fixing. You might need to download MS Tools for Debugging in order to get windbg to create the stack traces app-verifier requests to assist in debugging, so grab that as well... This is the single best way to help solve this issue.
Ordinarily I'd say just send me a crashnow dump so I can see what's going on, but because the process is so badly messed up that won't work. You might be able to use the vista debug/memdump or whatever option from task manager to create a minidump of the process. I can use that to verify it's the same problem I've been trying to track down. This is actually far less useful than the app-verifier tracking because that might catch the problem when it occurs and not when it shows up later.
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