I get similar messages. Sometimes to upload 100 images, I have to restart the upload 10 times. Sometimes I can't upload a particular Smart Publish Collection for a month, it just won't upload, and then like magic, the next time it uploads.
Jeffrey told me via e-mail that his plugin simply reports the messages from Flickr, so any problems are problems caused by Flickr.
I think part of the problem is that Flickr's parent company Yahoo! is struggling, and the money and resources to maintain and improve Flickr just isn't what it should be.
I figured most if not all of the errors were on Flickr's end, but was also hopeful my screenshots might get seen by them and maybe spur some fixing action - you never know!
Thanks for chiming in.
Flickr doesn't read these forums