My girlfriend has a titus motolite fs. Gears shift fine majority of the time, but when in granny ring and two thirds up the cassette on a climb under pressure it is really noisy and sounds as though it is rubbing on something or incorrectly set up.
The bike shop did fit a medium cage rear derailleur whereas I have a long cage on my bike so wondered if thats the problem as we run triple 11-34.
Any ideas or help would be much appreciated.

Check the limit screws on the front mech.

check the B-tension screw, sounds like your top jockey may be rubbing on the cassette teeth, you may even see it juddering as it does it.Shadow type mechs are very sensitive to this adjustment, especially with a 34t.

I just had a similar problem swapping from a long to medium cage mech, the chain was to long and when in the granny the chain folded back onto itselfs, removing 2 links from the chain solved this, but you will have to be careful of big-big gear combos, but thats what you get for running a medium cage mech on a triple set up.

-Check mech limits set up correctly
-Check that the mech isn't extended/stretched too far
(b-tension)
-Bear in mind that you might always get some rub in extreme gear combinations

If you need help setting up the mech then look at the Park Tools website:
http://www.parktool.com/repair/readhowto.asp?id=75

Check the front mech hasn't twisted round slightly. even a small slip of a mm or two can make a big difference

I used to run triple 11/34 with a long cage XT mech and found i could neve eliminate the rub from the top jockey wheel no matter how i set it up.
Went back to 11/32 and found it a far smoother experience.

Just read this post – is JLC calling me a 'heavy load'??

try new cables it could be trying to change as the suspension compresses mine does this when the cables are goosed