Fundamentally it is an apple itunes server issue - if you have a lot of downloads the "check for downloads" request can take longer than the default windows internet connection timeout setting - which is 30 seconds on more recent versions of windows.
You can work around it though - without requiring apple to "segment" your download list, by adding a windows registry setting.
Apple re-enabled my downloads after I was burgled and then I was stuck - my "check for downloads" was always timing out - and the support guy had no clue - so I went digging, and found a a microsoft article here
http://support.microsoft.com/kb/181050 which tells you how to change change that default timout value by adding a registry setting. Besides adding the ReceiveTimeout setting detailed on that page - I also changed the KeepAliveTimeout - just in case.
HKEY
CURRENTUSER\SOFTWARE\Microsoft\Windows\CurrentVersion\Internet Settings\ReceiveTimeout
which I set to 180000 milliseconds (3 mins)
HKEY
CURRENTUSER\SOFTWARE\Microsoft\Windows\CurrentVersion\Internet Settings\KeepAliveTimeout
which I set to 181000 milliseconds (3 mins and 1 second)
Use regedit to make the change - both settings are DWORDS with decimal values. You'll need to restart your PC to apply the change.
After the change and restart and one initial failed attempt the request for downloads worked - when the apple itunes server responded after 2 minutes !!