Several things come to mind but they might be trivial, relative to the changes you are seeing.
First - I'd look to see if temperature and humidity can affect your measurements. They do have some effect however I do not know if the differences are so small they cannot be detected - or if they are significant.
The readings are taken in the same room always.There is a window on one side,however,the window is always closed when taking the readings.I have noted that when it is sunny or cloudy,it does make a little difference to the readings around 0.2 microvolt difference depending on the time of the day.
Second- are you sure that the power output of your transmitter is constant? Could the unit be warming or cooling - or possibly drifting in frequency?
I usually take the reading as soon as the unit is on and then let it soak for 30 minutes and again take the readings.There is a heat sink so the temprature variations are negligible.
Are there things in close proximity to your test gear that could affect the transmitter? It needs to see a relatively constant load - if not the output would be affected. At microwave frequencies even non-metal objects have an impact
There is a window on one side and multimeter and dc power supply on the other side.However,the test gear is brought in front of other obstructions so I guess,they dont affect the readings.
I am a little perplexed besides,I want to know,if I can,an alternate method to test the range fo the microwaves without going outside.