Actually flat wound strings are really dull and should not harm your fingers, unfortunately they tend to sound really dull (unless you are Steve Harris from Iron Maiden who uses flat wounds on a P bass and sounds RAD) but then again I like my basses to have a brite bite to them so I stick to raound wound.
If you do not like the finger noise try cutting your nails, turning the treble down, using a pick, or modify your technique.
There may be many ways to help your problem.
clif
PS Freak sorry to hear about your hands, make sure you see a doctor, my friend plays bass and has tendonitis so do not be too discouraged. Try using way way lighter gauge strings, that really helps my friend and see a MD.