Its more likely you have a clash with the drive letter assignments of the partitions. In other words a Hd partition may be set to D: but a Dvd or Cd rom in the system may of already requested the drive letter.
A clash if you like. Its still there you just need to push the drive letter assignment up in windows if it is not showing as a logical partition with in windows. You can change the logical drive letter of the partition in disk manager.