I'm glad I did a search and found your thread. I've experienced the SAME exact problem. When stopping at a red light, the car seems to stutter and the RPM's drop as if I was driving a manual car in gear and letting off the clutch. The car continues to shake until the light turns green and I accelerate. I bought my IS250 AWD brand new, and I've experienced this problem since ~6K until now (i have 55K). I've brought the car into the dealership numerous times (probably a dozen times or more). On many occasions, they indicated that they couldn't replicate the problem but it seems to be a problem that Lexus has made note of and they are "trying to find a fix" (according to the service adviser). Many times, they've run some solution through the engine to clean the valves. This is a temporary fix and it seems to come back soon after. I got tired of the same story, so I told them it was a problem and I didn't buy a Lexus to deal with it. They asked if the lead technician could take the car home to see if the problem would present itself. When he took it, the technician FINALLY replicated the problem and said he didn't know what it was. He apparently took a snap shot of the computer (i think through the OBDII) to send to Lexus for investigation. In the mean-time, they ran that solution through the engine to clean it again.
Fast forward to recently when Lexus announced the problem with the valve spring issue. I called HQ's because the 250 wasn't specifically named, but I figured it could be related. HQ indicated that they thought the problem was unrelated but I should try taking it to another dealership for a 2nd opinion. Another issue is scheduling warranty work at this other dealer (another problem in itself), but I finally have an appointment to take it in tomorrow. Apparently they have some "field technician" coming from Lexus HQ that's on the Lexus IS assembly line that knows the car in and out. I'm hopeful that they find the problem and fix it, or else I'm going to sell the car. I'm tired of the run around for a defect that they can't seem to fix.
