Does the font contain a feature except from the kern feature?

Yes, it contains 'liga'.

I am aware of OT fonts needing 2 features for them to work properly.

Proposal: Destroy your outlines by using an effect action and upload your font (the VFB file, if you are using FontLab). That’s the easiest way to detect the problem. I don’t know, if I find the time to check it, but I have Indesign CS2 and CS3 parallel installed on my Not-Mac.

Run the FontQA macro and see what it tells you.
http://www.fontqa.com/

Sometimes, if there are any problem of any kind (contour direction, glyphs naming, whatever..) the OT features fail to work on some windows programs.

That's happened to me on the Lobster betas, but once fixed all errors and warnings, the OT features started working again, like magic.

Now I always run the FontQA and test everything twice before releasing

I have just received a reply from the client:

Happy New Year.
Excuse the delay, bit of a lull over christmas.
I'm afraid I owe you an apology. We have found what the problem was, and it was never your font.
When my colleague carried out the test with the old and new versions, he found they were exactly the same -- and very nicely kerned.
We went back to the tests I sent you in the first place, and the difference was that mine were created with our headline paragraph style, which was all over the place as you saw. The error was in a style which was nested within the main headline style, which actually turned kerning off. Why that should have been done, I cannot fathom.
So I owe you a big apology for wasting your time, not to mention casting aspersions on your typography. It wasn't the horrid PCs, or even our obscure software, but a traditional human cock up. Good thing we had someone else do the tests.

I had suggested that kerning may be turned off at the outset, and so that proved to be.

Thanks to Arno and Pablo and Karsten for your suggestions.