Hello ehud,
It sounds like you are using the old GUI. The inductance value is not being calculated correctly, but the FCOUNT value is. If you right click on the plot and select "Toggle data type" it should show Frequency Count data. From here you can directly calculate the sensor frequency from page 12 of the LDC1000 datasheet:
For example, if you use an LDCLK of 6MHz, RESPONSE_TIME of 6144 (default GUI setting), and get an FCOUNT of 3410, the sensor frequency will be calculated as 3.6MHz. Then using equation 4 on pg 13 of the LDC1000 datasheet you can calculate the inductance:
Using fsensor of 3.6MHz and C of 100pF (default EVM populated value), the inductance computes to 19.5µH, which is the correct value. If you change LDCLK to 3MHz you should notice the Frequency count drop to about half of the value (~1705). Running through the same calculation with the new LDCLK value and FCOUNT value you will arrive at the same numbers.
Alternatively, you can download the new GUI from the LDC1000EVM product page: 
Regards,
Luke
