I'll start off by my saying my tranny is manual.
When I shift to second gear, it doesnt shift very smoothly (Jolts a little) and this makes it very hard to do a quick/smooth shift. I always have to clutch very slowly to get a smooth shift (around 2-3 seconds). All the other gears I can shift as fast as I like and they are fine...
It reminds me a little of shifting/clutching at a high RPM (ie You can feel the engine disengage and then reengage quite sharply as there is alot of power suddenly going through the wheels..), but this is in second gear changing around 2.5/3k rpm..

The problem seemed to go away after the last service, but only for a week or two.... :(
Anybody know what could be wrong?

Synchros in 1st -2nd usually wear quicker than others. Ive had 2 manual magnas (te 3.0 and tj sports) and both do the same thing. Somedays they both changed like a dream though. You could try an additive in the gear oil and see if that makes a difference. Nulon G70 is pretty good.

I would point the finger at the drivers side engine mount. That was the problem in mine. It is a frequent issue with that mount and the rough gear changes are one of the symptoms.