Okay, so on the first 1-2 shift of the day, my Tracker's 3 speed has a weird shift.  It usually is kinda slow and drawn out.  It starts, I can feel the revs kinda die down, might jerk a bit, and then slowly goes into the next gear.  Sometimes it jerks just once, other times it sorta seems to throb a bit and then go into 2nd.  After that it shifts fine 98% of the time for that drive.  If it sits for a while the next time I drive it does the same thing on the same first shift.

151,000ish on the clock, just had it's first pan drop and filter change in at least 50,000 miles and 4 years.  Nothing too scary in the pan or on the magnet but it was obvious it had been a while since the fluid had been changed.  Been doing this for the last month I've owned it.

I recently bought a tracker in January that has 180km on it and I have no idea as to how frequently it was changed. I plan on doing the transmission fluid and filter this weekend so I have been trying to read as much as I can about it. Some people recommend not doing the transmission service if you haven't done it in a long time while others say you should. From my understanding you get a build up of varnish and what not in the tranny. When you change the filter and put new fluid in the new fluid acts as a detergent and washes out all that old varnish and plugs up the new filter rather quickly.
 I bought two filters and enough fluid for two changes. I plan on doing the fluid and filter, drive it for a week and then I will drop the pan and do it again and have a good look at the filter.
 If I were you I'd try changing the filter once more. They are cheap and it would be good to see if this is the actual case......it makes sense to me.
  Maybe others on the board will have a better idea.
Good luck
Jim

Yeah I'm thinking about doing that.  I need to do the GV soon so I might as well do them both.  Sometimes I really miss my manual transmissions.

Check your pan, does it have a drain plug?  The 3 speeds don't have drain plugs so changing it is a bi$ch.  You'll have to disconnect the front driveshaft at the diff, secure it to the frame on the p-side, and still you'll likely end up with an ATF coated catalytic convertor and ATF all over the floor.
I bought a drain plug kit from www.SummitRacing.com and put that in when I did the flush.  Easy, simple, and cheap.  You can likely get them from a local supplier of B&M products.  Word of advice though, don't put the plug on the passenger's side of the pan.  I saw that there was a big empty space above the pan there so I just drilled the hole and bolted the plug in.  Then I went to put the driveshaft back on and I realized the 'shaft goes directly under my new plug!  Luckily I have about a quarter inch of clearance and so far, so good.  It's IFS so you don't have to really worry about the diff moving and unless my engine/transmission/t-case mounts go out there shouldn't be enough play in the system to make it hit.  Irregardless I'm keeping an eye on it for a while.