I found the following link. Excellent article.
http://www.djmelectronics.com/articles/emc-antenna-parameters-p3.html
This covers antenna factor and a lot more.
I had to wonder if you are feeding the transmit antenna symmetrically?
For example, if you fed it directly with a coaxial cable, one end of the loop would be effectively earthed so the radiation would probably not be symmetrical.
If you rotate your coil by 180 degrees and get different results, the radiation is not symmetrical.
The reference above refers to using the test setup in an anechoic chamber to avoid reflections.
You might find the following site useful too. Not that it will fix your present problem, but it is a great calculator for large single turn loop inductance.
http://www.qsl.net/in3otd/ind1calc.html
The inductance of your large loop would be nearly 50% greater than that of your small loop.
1.48 uH vs 1.04 uH.
I did a check on the self resonant frequencies of your loops. The big one would resonate about 180 MHz and the small one would resonate at about 280 MHz, assuming a tube diameter of about 10 mm. So, this is sufficiently high in both cases to not matter.
This was done with Eznec, an antenna modelling program.
Does the shielding on your loops have a gap somewhere around the circumference? I think they are supposed to have this to avoid circulating currents in the shield.