CGI::uploadInfo() should return a hashref to all the uploaded file's headers. I don't think there is anything unusual about the filehandle returned by upload(). I'm suspicious of shoving your handle into IO::Seekable if it isn't already, but the buffer should be seekable so I don't think that's contrubuting anything to the real problem.

You appear to have a lot of external variables in your sub. Are these always doing what you expect? Consider the effect of closures. Using strict may help sort things out.