I wouldn't be surprised if the problem is with the aircraft. The radio frequencies both Comm and Nav are divided into two. One dial sets the whole numbers and the other the fractions.
This is in fact already hard coded into the sim but developers sometimes like to do things their own way and this can lead to errors.
If the a/c developer lets the sim do it then the code is
<Click Event="NAV1_RADIO_WHOLE_DEC" Repeat="Yes"/>
<Click Event="NAV1_RADIO_WHOLE_INC" Repeat="Yes"/>
Then the sim reads the numbers in three steps to divide it correctly into integer, tenths and hundredths like so
<Value>(A:NAV1 ACTIVE FREQUENCY,MHz) 100 * 1000 / 10 % flr</Value>
<Value>(A:NAV1 ACTIVE FREQUENCY,MHz) 100 * 100 / 10 % flr</Value>
<Value>(A:NAV1 ACTIVE FREQUENCY,MHz) 0.001 + 100 * 10 / 10 % flr</Value>
Note. This example is in XML which uses reverse Polish notation. Which is why nobody on the planet understands it!!
This would certainly not cause a problem with PF3 and perhaps not with MCE. As I don't have MCE I can't confirm how the developer reads frequencies.