Ok, if you don't need the chek in check out functionnality you can disabled it.
If you want it you can set it by codes throw Web service, I found this sample :
public static void UpdateListItemCheckOut()
{
listservice.Lists listProxy = new listservice.Lists();
listProxy.Url = "http://SERVERURL/sites/tester1/_vti_bin/lists.asmx";
listProxy.UseDefaultCredentials = true;
bool success = listProxy.CheckOutFile("http://SERVERURL/sites/tester1/tester2/test.txt", "False", string.Empty);
success = listProxy.CheckInFile("http://SERVERURL/sites/tester1/tester2/test.txt", string.Empty, "0");
}