From what I can see it's complaining when [vfs read] fails because of a missing a file / directory on a PRE_STOR call to the ioNinja script. Now, what's causing that and why is a good question, and I'm not sure why it would only happen for some extensions and not others...
The first thing I'd like to know is it you upgraded to the latest stable version of ioNinja? Then I'd like to know if it happens with every directory you create and try with those extensions? Only some of the time? With other extensions? Is the directory good for uploading other files? Dir hasn't been nuked behind your back? How long do things slow down /timeout? 10 sec? 30 sec? Single uploader to directory? When things get stuck can you verify that the file exists by trying to list the directory via another login?
Gather some more info if you can, but I'm pretty sure this is a better question for o_dog and ioNinja.
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