Assuming that you were squawking 7000, then it is possible that the ATCO may have had his radar set up to filter out 7000 squawks. (Why he would do this in a LARS or airfield environment i don't know, but i believe that it is used by area controllers to avoid loads of unwanted returns below CAS from obscuring airways traffic).
If you're squawking 7000 then as you have not been identified and had your mode C verified the controller cannot rely on its readout, but would normally say something like "unidentified traffic in your 12 o'clock tracking left-right indicating 3000 ft not verified".
You may have too low for the secondary radar to get a good signal. Do you know where you were in relation to the radar? It may not have been at the airfield you were talking to,but could be some distance away. I expect you know that the farther away from the radar aerial you are the poorer the low level coverage is. Eg Birmingham. secondary radar is on Clee Hill (about 30nm west of the airport) so if you are 30nm east of Brum....
Don't know if any of that helps...have you thoroughly checked out the performance of you x-ponder?