Well, he writes about considering the five episode season an insult and feeling frustrated that the harder the Torchwood team worked, and the higher the ratings they brought the BBC, the less respect they got. IIRC he also says he found Davies' attempts to argue that it was a sign of prestige to get this great one-week drama slot unconvincing (and, indeed, Davies has since admitted he was trying to be upbeat and positive for the sake of the team about something he wasn't hugely happy about himself).
The other thing is that writes about finding Euros Lyn very difficult to work with. Their problems seemed to be grounded in Lyn's desire to get an underplayed, more introspective performance out of Barrowman and Barrowman's push-back that such an approach was wrong for Jack. The sticking point was that Lyn didn't so much make the suggestion, as mount take after take after take after take till he got what he wanted - leading IIRC a frustrated Barrowman to storm off the set in a temper on one occassion.
Reading between the lines, it seems like Lyn took inspiration from Nicholas Meyers' comment on making Star Trek II -- that the key to directing William Shatner was to make him do so many takes he became too tired and beaten down to 'do his William Shatner routine' and simply acted instead.
Which, in both Shatner and Barrowman's cases, seems to lead, ironically, to the director to get the best performances out of them being the ones they got on with the least well.