A lot of confusion here, let's do it point by point
The minutes are available on the internet:
http://www.injusticeinperugia.org/Verbale_6_nov_01.45.pdf
If you please look at the top of the document there is written:
Transcript/minutes (Verbale) of summary information (sommarie informazioni) from person informed of facts (i.e. a witness)
These are the minutes of the witness interrogation (i.e. taking summary information) that Donnino is being asked about in the trial transcript. Ghirga notes that only opening time of the minutes is written down, unlike the minutes of Raffaele's interrogation that recorded both opening and closing.
This is the confusion I'm talking about.
a person informed of facts is a witness, not a suspect (l'indagato). Just look at the interview you linked:
Because it's written at the top of the document?
Let's say Mignini wasn't precise
The document records the opening of the minutes at 1:45am.
Reading the transcript of Donnino's testimony it's all about this 'funny question'. The defence asks her when exactly had the accusation been made and she cannot answer. She only says it was after the 1:45 interrogation started.
There is no record of when the accusation had been made, we can only time it by Donnino's remark that after that there was only a brief pause and then Mignini took over. This time is on record in Amanda's "voluntary" declaration of 5:45am.
Of course inspector Giobbi also gives the time that confirms what Donnino revealed. The interrogation lasted from after 10 pm to around 5 am.