Do you have some more details? (You should not expect that generating a font and then importing it will produce you exactly the same VFB with which you started. Some things will change because of different data structures, especially when it comes to AFDKO-syntax features and FLS5-syntax classes.)

Here are a couple of screen grabs that illustrate the problem.

The source VFB:

and

The generated TTF:

Notice the difference in the classes has adversely affected the kern pairs available in the font.

Notice the difference in the classes has adversely affected the kern pairs available in the font.

No. Notice that the LEFT checkbox for class kerning of the A is unchecked in the generated TTF: that's what's causing the problem...

Hey Nick, Yes, that is the problem but I'm not the one doing that. When the font is generated from FontLab that is the result.

Delve,
check if the kerning is really lost in the generated font (basically, that’s what you care about).
Probably, it is only happening during the re-import to FL.

Could you please check the relevant pair in InDesign?

Thanks Frank and Karsten. Yes, the kern pair is missing in InDesign. I have V in the Y class and one of the changes in the generated font is that it no longer has a class for Y, which in turn effectively deletes the A/V pair as well. Weird.

Update:

When I tried generating the font using the same VFB with FontLab on a PC, I got the Warning reported here: http://www.typophile.com/node/27336

Note: the Mac version of FontLab did not give that warning.

So it seems there may be a duplicate class or some similar error in the classes. Now it's just a matter of finding it...

You might try using the "Clean Up Classes" function in the Classes Panel...