Yes, I get this error for every download of a file as well. I've looking into this. It seems to have to do with calling:
HttpContext.Current.Response.Clear()
HttpContext.Current.Response.ClearHeaders()
HttpContext.Current.Response.ClearContent()
which occurs in Download.aspx.vb DownloadFile() method. However, looking at the source code, that seems to have been replaced by a call to StreamFile(). So, the released DLL in 3.01.09 is behaving like the older code was compiled, then the newer version was included in source code package.
I recompiled the source so it would now use the StreamFile() method and now I get other types of errors. I think due to use of System.IO.Stream in a medium trust environment.
So, its my belief that the released DLL of Repository 3.01.09 is called DownloadFile() which triggers the cookie error and that the new version of the source code has different flaws.
I'm going back to the 3.01.09 DLL for now and just living with the errors in the error log.