Bill, you may find my #179 interesting.
A more detailed timeline -
John Winant, old time Red, replaced Old Joe on October 22, 1940 as Ambassador to Great Britain.
http://www.usembassy.org.uk/rcambex.html
It is commonly held that Joe Kennedy Sr. was replaced by Roosevelt because Old Joe was very publicly saying that Britain was beyond hope and that America should stay out of the European war.
The Moscow Line from the Ribbentrop - Molotov military alliance pact until the June 1941 invasion or the Soviet Union by Hitler was pro-Hitler. The United States was to kept out by all Communist means of the "European War".
So far Old Joe Kennedy meets the "quacks like a duck" test.
Joe Jr. and JFK joined the military, certainly at Old Joe's urging, in late 1941. (Unfortunately I cannot find the exact date.) JFK could not enlist because of his back injury and other health problems and Old Joe had to pull strings to get John a health waiver. This probably took a month or two. So JFK had to be trying to enlist in September or October of 1941 at the latest, that is, a matter only of weeks after the changed Communist Party Line followed Hitler's invasion of the Soviet Union. The Moscow Line shifted from an isolationist to an all out pro-war position in the USA overnight.
So, we have "Quacks like a duck" and now we have "Walks like a duck". So therefore we are seeing a duck, right? Certainly enough evidence to persuade an intelligence analyst something was fishy.
Thanks for your follow-up. JFK's Wikipedia entry says the back injury enlistment obstacle you mention occurred in spring '41; also I recall that JFK had published his book on Pearl Harbor the previous year. I think his father was probably more concerned about grooming him for a future political career than in making sure he followed his own political positions. I'm not aware of any evidence in Joseph or JFK's FBI files indicating any Communist connections during this period, and there were extensive security reviews of both of them so I'd think it'd have been noted. At this time the intelligence community--both British and US--was mainly concerned about Joseph's Nazi ties, and there was also a scandal with JFK having a romantic relationship with a Nazi spy, Inga Arvad, in 1942. As far as I know (off the top of my head anyway--I could be forgetting something) JFK didn't pick up any strong left-wing associations until he started running for President and taking advisor recommendations from former members of the FDR/Truman State Department, which had of course been heavily compromised.