Company flying flag initially ran off at sea (7)
I believe the answer is:
baffled
'at sea' is the definition.
(I've seen this in another clue)
'company flying flag initially ran' is the wordplay.
'company flying' becomes 'ba' (I can't justify this - if you can you should give a lot more credence to this answer).
'initially' says to take the initial letters.
'ran' becomes 'fled' (to flee is to run away).
The first letter of 'flag' is 'f'.
'ba'+'f'+'fled'='BAFFLED'
'off' is the link.
Can you help me to learn more?
(Other definitions for baffled that I've seen before include "Perplexed" , "Frustrated" , "Completely mystified" , "Confused" .)