RF dielectric measurement of a sample
The best substrate dielectric measurements are made by etching your own test pieces onto the substrate under test. That way, you have only one material in play.

It sounds like from your question, you are using patch antennae to couple to a substrate under test. What the VNA will measure is the perturbation of the patch antenna when loaded by the substrate under test. You need to analyse the whole system to get any meaning results from the measurements. Depending on the measurement geometry you use, this may be more or less sensitive to geometry and analysis errors. That's why it's better to use only the substrate you are testing.

Rogers 4350 is the 'go to' material for many applications in the GHz. It's readily available, and can be processed using the same workflow as FR4, and indeed is frequently bonded with FR4 to make a hybrid multi-layer board.