I would log a Service Request with Oracle, as the error could arise from anything (basically a piece of memory is being accessed, but an object does not exist), so it could be a bug, or it could be content that wasn't created correctly.
I'm getting the same error in UPK 11.1 (multi-user environment) when I attempt to publish the player. I'm wondering if it has something to do with importing the .ODARC file from UPK 3.6. I noticed the system folder files in the library were replaced with older versions after the import.
I have just checked, and there is a fix for this issue through myoraclesupport (Object reference not set to an instance of an object).
Log onto the support portal, and apply the patch - that should solve your issue.
See my message above - fix is available through Oracle.
With regards to your system folder files...
When you import an ODARC file into UPK, it still asks you if you want to create an "import" folder (if you have not already created it), and it also asks if you want to overwrite exisitng files.
You must have selected the option to overwrite existing files, as I cannot think of any other reason why an import would overwrite system files.
When you perform an export, rather select the appropriate files/folders and then export the selection - at least this may help not exporting system files and overwriting system files in the other system.
I just came back to the forum and saw your post. I managed to get it working, but I'll look into the solution myoracle support has posted.
I ended up deleting my new 11.1 profile (that I was having issues with), converting my original 3.6.1 profile again and reimporting the 3.6.1 ODARC file. However, this time when I did the import, I selected NOT to overwrite the content -- that seemed to work. I can publish the player now without that error coming up.