ORIGINAL: Ian R
In your example, it looks like the search roll number for the 3 section (only) which contains the CV plane is modified to 4. The search number for the 2 section is not modified, and remains a 2. CW rolled a 3. Also there were no convoy modifiers of -1 to the search die roll, so was this an interception combat?
The RAC says (11-5-5):
The search numbers can be modified (see 8.2.4) by +1 if the weather in the sea area is fine, rain or snow, and if the section contains one of your side’s NAVs or undamaged CVs (CVPiF/SiF option 56: a CV must have a carrier plane on it).
(my emphasis).
Edit: after reading the example in the right hand column of RAC page 54, the failed Italian search roll should mean the allies can include sections 0 and 2 and exclude 3. That would not include any allied units in the 0,1,2 sections (rolled a 3), but it should include the Italians.
The Commonwealth carrier air unit has no air-to-sea factors so there is not a +1 for that. Since the search number went from 2 to 3, the +1 must be for the Italian convoy. Therefore, this is not an interception combat. Another clue is that the Commonwealth is the Phasing Side, so the Italians can't moving units (an exception would be aborting from a naval combat, but none of their units is marked as aborting).
But an interception combat could have explained why some section boxes were excluded. That was a real good try.
If the units in the 2 section were aborting, then they would have been excluded. But they are not (no status indicators are lit for that condition).
I am not sure why the program omits the Italians in the section 2 box. As you can see from this discussion, the program makes a lot of calculations when determining which units can be included in a naval combat.
I need a saved game with instruction on how to reproduce, in order to debug this.