You can scan yourself, as long as one of your fleets are returning home. However, the description of the scan (on the waves page) says: This scan can be used if you have a fleet travelling from you to the target. It will reveal any other fleets traveling to the same target.
So it does sound like you are not able to scan yourself (notice that it says "from you to the target", while a returning fleet is from the target and to you. Actually, it would make sense if the target could do a JGP on you, as the fleet is on the way from him to you.)
Edit: the description in the manual is actually correct. On a side note, I happened to check the FAQ on the portal yesterday, one of the questions is about Sector Scans