just had a look about and this seems to confirm my suspicion, its an article from when cardiff got to the FA Cup final
http://www.dailymail.co.uk/sport/footba ... A-Cup.html
"Dave Jones' side have reached the semi-finals of the competition for the first time since 1927 - the year they last won it -
but under current FA regulations they will not be nominated to represent England in the UEFA Cup if they lift the trophy."
The Bluebirds come under the jurisdiction of the FA of Wales, even though they choose to play in FA competitions.
This leaves them in limbo as neither association can nominate them for Europe - the FA because Cardiff are Welsh and the FAW because they do not play in their competitions.
Cardiff chairman Peter Ridsdale had hoped the FA would put them forward but the governing body have moved today to reiterate their regulations.
An FA spokesperson saidt: "Our position remains unchanged and should Cardiff win the FA Cup this season they would not be chosen as the FA's nomination for European competition.
Obviously not exactly the same situation, but it seems to confirm that the FA can decide who to nominate for european competition and, had they felt so inclined, could have nominated cardiff.
If the FA can decide who to nominate from the FA Cup then it would make sense if it is the premier league who decides who is nominated from the prem, and i reckon they will want liverpool in if possible