I'm also still having this issue, stragely the only reason I really need this is for Podcast updates, why can't apple let the iOS device auto download and avoid this issue for me (been playing with iCatcher, however I need to remember to open it and keep it active enough to complete downloads).
The only fix I can find is to kill iTunes and restart twice a day (just before I go to bed & just before I wake up). This allows my phone to sync at least once a day without issues. I've commented out the section that checks if iTunes is running, as I don't care because I want to to start anyway, I've included for your reference. This is not a clean workaround, but the best one I can think of given when the error occurs, the pop-up window locks iTunes from any active updates & using non force kill doesn't close it.
Just save as a .vbs file & use taskscheulder to setup as per your preference.
'
Set WshShell = WScript.CreateObject ("WScript.Shell")
' Set colProcessList = GetObject("Winmgmts:").ExecQuery ("Select * from Win32_Process")
'=============================================================================== ===============
' For Each objProcess in colProcessList
' If objProcess.name = "iTunes.exe" then
' vFound = True
' End if
' Next
' If vFound = True then
WshShell.Run ("C:\Windows\system32\cmd.exe")
wscript.sleep 50
WshShell.sendkeys "taskkill /F /IM iTunes.exe"
WshShell.SendKeys "{ENTER}"
wscript.sleep 50
wshShell.SendKeys "exit"
WshShell.SendKeys "{ENTER}"
wscript.sleep 50
sub shell(cmd)
' Run a command as if you were running from the command line
dim objShell
Set objShell = WScript.CreateObject( "WScript.Shell" )
objShell.Run(cmd)
Set objShell = Nothing
end sub
shell "c:\Progra~2\iTunes\iTunes.exe"
' End If
PS - I also decided to not sync my iPad over WIFI, this seems to help reduce the number of issues & I really don't need to sync it all the time.
Edited to include iPad statement.