It does sound like you are encountering bizarre error messages, and they should be much easier to avoid than the attempts you are making.
Just for clarification, you mention MP4, so I am guessing you are speaking in regards to submitting the lower quality proxy as opposed to a final clip after approval. MP4 is only acceptable for that preliminary proxy stage. And by the way, one thing that really tripped me up at first was that the page design of the upload page seems to imply that one can upload a full quality clip for approval - but I was told that one must get the lower quality clip approved before one submits the higher quality clip.
So, assuming that you are talking about the proxy stage. If not, I would try doing the Motion JPEG or Photo JPEG route and see if the rrors go away.
The only thing I would initially think is that in the process you are mixing PAL frame rates with NTSC pixel aspect and resolutions. However, given your length of experience, that doesn't seem likely.
Here is what I would do (and again, assuming you are using MP4 for the proxy stage) as a test - because if this doesn't work, there is definitely a bigger issue going on outside of what is within your control.
Try to generate a clip (as opposed to using a captured clip in a particular native CODEC) in the format of your choice (PAL 25 fps or NTSC 29.97 - native reolution) by either using something like After Effects or simply using your editing application to create a balck (or any color for that matter) clip and then export it as frames (this way you just end up with raw data without pixel ratios or interlacing being an issue inherently - it's just pixels waiting to be interpreted). Not that this is a way one should have to work, it just starts to eliminate some variables. Take that clip into Quicktime and export it as straight MPEG 4 (there should be an option for this OTHER than h.264) being SURE that you are not applying any other changes (I know that sometimes my Quicktime seems to "default" to a nonstandard size when I export to MP4 - making it half size for example - that has tripped me up before).
Now, try to upload that (you can always cancel the upload afterward if it works). If that clip STILL generates an error message you are defitienly experiencing a technical issue you should not be that has nothing to do with your workflow or clip parameters.
Anyway, that's what I would do, if you haven't already done something like that.