More stuff on the cutting room floor I'm afraid. And, I’m not able to access any books at the moment. However, it would be as well to remember two aspects of the conflict at that time. These are, firstly, the Milan and Berlin Decrees and, secondly, the Orders in Council. It is my understanding that a blockade was in place, not as a result of the presence of the Russion squadron, but as a result of Napoleon’s demands on Portugal in order to implement the continental system in full, insisting that:
“unless Dom Joăo acquiesced to Napoleon’s demands in full, declared war on Britain, recalled her ambassadorial presence from London and dismissed that of Britain in Lisbon, detained all British residents, sequestrated their goods and property, and closed all ports to British shipping by September 1st, France would invade Portugal. (136) A further request, that the Portuguese navy be placed at Napoleon’s disposal, was already known to Dom Joăo’s ministers - who had forewarned Britain of Napoleon’s designs on the Portuguese fleet as early as May 1807.” (137) NB my emphasis here, not in the original.
So, it was the ban on trade with Britain, and which Portugal was forced to acquiesce to and implement, that prompted the blockade as part of a broader shift in naval strategy away from the focus of the Western squadron and the Bay of Biscay (and northern France, Holland etc), the Baltic, towards northern Spain, Portugal, souterhm Spain and (your favourite subject) the Mediterranean. It is also worth considering the substantial mercantile traffic into Lisbon, of whatever nationality and ultimate destination, given its important role as entrepôt for Brazilian raw materials, goods and produce. For which see the various references in my MA, pp. 54-55 and, of course, Robson, Britain, Portugal and South America, pp. 179-195.
136. See Harold Livermore, ‘Portugal on the eve of the Peninsular War’, in Paddy Griffith (ed.), A History of the Peninsular War, Vol IX, Modern Studies of the War in Spain and Portugal, 1808-1814, (London : Greenhill, 1999, 385-98, especially pp. 394-95, Soriano, História da Guerra Civil, 1.a época, vol. 2, pp. 644-48 and, for details of the demands, ibid. vol. 3, pp. 587-594.
137. For the suggestion that Britain knew of Napoleon’s designs on the Portuguese fleet, see Richard Glover ‘The French Fleet, 1807-1814: Britain’s Problem; and Madison’s Opportunity’, in The Journal of Modern History, vol. 39. no. 3, 233-252, in particular see p. 3, and n3, where the author cites The Diaries and correspondence of James Harris, first earl of Malmesbury, vol. 4, p. 391 and Harold Temperley, Life of Canning, (London, 1905) in which the author offers verification of the general accuracy of Malmesbury’s information regarding the Portuguese fleet.
I have a pdf of Glover's article if you'd like it.