New customers frequently are concerned when SynthEyes calculates a focal length that does not match the value recorded on set, even though the match-move is good. Here's why.
Focal length is only half a number. It can be computed from the field of view only if you also know the exact back plate width (you don't). SynthEyes calculates the (horizontal angular) field of view, which is the single underlying number.
So unless you have properly set the exact back plate width on the shot settings panel during shot setup, or via Shot/Edit Shot, the displayed focal length will appear incorrect, even though field of view and overall match are correct. The focal length will be right—for the given back plate.
Here's the next problem with focal length: you don't know the exact back plate width, unless you do some lab-grade testing. You may be able to get an approximate value from the camera manufacturer, but there are many underlying manufacturing details that limit the utility of that number. And even still, a quoted value will be much less accurate than SynthEyes-calculated field of view.
To cap it off, that on-set focal length value isn't necessarily accurate either. Camera manufacturers have quoted +/-5% accuracies on lens focal lengths... again way less accurate than a SynthEyes-calculated field of view.
So where does this put us? First, for accuracy you should always be concerned about field of view, never focal length.
What use are on-set focal lengths? If you have a decent estimate of the back plate width (perhaps from a "good" shot), put that in. You can then roughly compare the on-set and calculated values. If you've got 46 and 50, great. If you get 22 and 50, you should investigate why the discrepancy is so large.
And in rare circumstances, namely object tracks where the object is small in frame and does not produce the parallax shifts needed to calculate a usable field of view, you might need to use your on-set focal length value on the Lens panel to set the field of view directly.