M4V TO MP4 WORKS BUT CONVERTED DOESN'T. Is this weird?

Bit of a mystery here. My second post to this fab website and I think I made need a guru to answer this question.

I have an original ITunes film which I can change to an MP4 just by changing its extension. The MP4 works well in Quicktime etc and all other media players like WM12, VLC etc. Clever Huh?

This is the bit where I get confused. If I then use 'XMedia recode' and shrink the file, oh tried Handbrake and loads of others too- the file no longer plays in Quicktime only.

BUT, if I change the extension back to M4V, the film works fine in Quicktime. Change it back to MP4 and it doesn't work!

I have looked at Mediainfo after conversion, the original file and the new file are exactly the same (other than the new file being a little smaller).

So to save me going bonkers, what is or isn't happening?

:(

Greg