Try being faster with your shifts, as in move the stick and clutch faster. Many newbs focus so much on what they're doing that they never get past the mechanical movements into a more fluid motion; many let the revs drop too much on up shifts and not enough or too much on down shifts.
If you're in an S model it will be even more difficult to master, as the gear ratios are not evenly spaced; the lower gears are taller ratios and the uppers are relatively close ratio, beig ~600 rpm apart...
Do not feel bad, I've driven non synchro trannies that were easier to drive smoothly than my S. I do however find that my smoothest shifts are my most aggressive.
Like others, I suspect that my engine mount has gone "TU" and is big part of the problem... I just bought a Schnell short shift kit and a new engine mount. When its all in place, if it's 70% as good as the 6spd in my GF's MCS, I'll be happy. Right now it feels completely unrefined compared to the Mini/BMW product, and that's after I put a solid flywheel in the MCS...that's saying something.
EDIT- I see while I was typing this on my tablet (takes a while), others rang in with the same advice...so there must be something to faster and more fluid...
