PDawg have you changed your fluid yet? Based on everything i've read, I firmly believe it has to do more with the fluid used than anything else.
Here's my take on this. Our manual states that GL-4 or GL-5 fluid can be used for the transmission, but the differential requires GL-5. From everything i've read, GL-5 is more "slippery" and less "sticky" than GL-4, so it may product better under very heavy loads (towing, continuous racing, etc.) but the synchros inside the tranmission have a harder time operating with the less sticky fluid.
Consider that the IS300 is the only car Lexus sells with a manual tranny, and the old car they have sold with a manual for a long time (since the manual SC300s anyway). I'm willing to bet that most dealers just stock 90 weight GL-5 fluid, and use the same stuff in both the differential and in the transmission. Technically the fluid meets factory spec. What I suspect is happening is that the synchros are having a harder time, which explains why downshifting into 2nd is problematic, at least until things warm up anyway. Double-clutching "fixes" the problem since the synchros don't have to do anything.
As for "trained Lexus Technicians" they're probably half-decent, but aren't experts on manual trannies. If you look through other posts, whenever people have tranny problems, it seems like they just swap in a new transmission. It's probably cheaper to do that for the small % of manual Lexus' that get serviced at the dealership, than to train everyone to repair in-house. We're a small minority (manual drivers) at the Lexus dealerships, so considering that 95-98% of the cars they service everyday are automatics, how much time/effort do you think really goes into research/training for our cars?
I'm not sure what the synchros are made of, but some sychros don't like GL-5 fluid over the long term. The fluids many have been seeing improvements with (such as redline MT-90) are GL-4 rated, and don't have friction modifiers like the GL-5 oil.
I'm going to swap out to a GL-4 oil over the next few days and see if there's a difference. I'm also confident that these cars probably came from the factory with a GL-4 oil ... my tranny was perfect (slightly notchy but nothing like what it feels like now) until the dealer changed the fluid. Now I can definitely tell the Synchros on 1st and 2nd have trouble engaging with downshifts. Rev-matching instantly fixes the problem (so it's not the lockout on 1st gear) ... rev-matching/double-clutching elminates the synchros.
The w55 is an ancient transmission, it was probably designed to work with GL-4, and technically would work with GL-5 (hence the manual's statement) but i'm guessing GL-4 is the way to go. I'm probably going to get some Royal Purple or Redline MT-90 and see if my tranny goes back to the way it was.
$100 - $200 seems high, i'm not taking it back to lexus. Their records show I had a tranny fluid change at 30k, great, according to them another one isn't recommended until until 60k. All I really care about is the warranty, and their computer shows i'm up to spec for another 30k, so they can't hassle me if anything breaks. The synthetic fluid should run about $30, and another $20-30 to have it changed (shouldn't be more than an oil change).
I'm curious to know what the Tranny would feel like with a non-synthetic GL-4 (non GL-5) with no friction modifiers, i'm guessing it would be fine. I haven't been able to find a fluid like that, and i'd rather just put some stuff in that I know works.