I've made a checkin changing a file, and the UI shows as if I have not done any change in any
file. The checkin has a delta manifest.

I think that the problem is that, the baseline manifest (the delta is based on)
has the same contents for the file as those I've committed, although in the
other deltas between the baseline and this delta, the contents have been
different.

The line of the manifest regarding the file, will look the same in the baseline
and in the new manifest, and so it does not appear there.