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CPU:0, GPU:1, PID:2196 (5)   Slot:3   http://milkyway.cs.rpi.edu/milkyway/   de_separation_13_3s_free_1_1164186_1303938523
Gpu: milkyway_0.52_windows_intelx86__cuda_opencl.exe, PID: 2196, Threads: 5

GPU was overheating quite a bit on this task at about 83C. GPU was using 2%. After I turned "Connect with BOINC Client" off it didn't change temperature at all.
Restart of TThrottle was needed to reduce temperature.

Just some clarification. Do you want 2 entries of separate tasks with "Connect with BOINC Client" off and 2 entries with it on?
Also do you want both entries to come from the same "instance" of TThrottle or restart between checking the "Connect with BOINC Client" setting?

Just blindly copying your example I have:
CPU:0, GPU:1, PID:4592 (5)   Slot:3   http://milkyway.cs.rpi.edu/milkyway/   de_separation_13_3s_free_1_1164206_1303938523
Gpu: milkyway_0.52_windows_intelx86__cuda_opencl.exe, PID: 4592, Threads: 5

Another Milkyway@Home task has finished for me and everything looks normal when the next task started.
This is with "Connect with BOINC Client" turned off.

plan class=(cuda_opencl) and Use=0.05C+1NV  for these tasks

Disabling the "Connect with BOINC client" seems to have fixed my problem.
After 1 Milkyway@home GPU task finishes the PID changes to the application of the next task.

The names of the tasks that are causing trouble all start with:
de_separation_10_3s_fix20_1_XXXXXXX_XXXXXXXXXX_X such as de_separation_10_3s_fix20_1_1000505_1303917207_1
de_separation_13_3s_free_1_XXXXXXX_XXXXXXXXXX_X such as de_separation_13_3s_free_1_1164154_1303938523_0

I seem to get about a dozen tasks from Milkyway at a time so I'll keep checking each time it switches task to see if the temp increases too much.
I've been using TThrottle with GPUGrid for the past 5 months without problems so I'd be interested to see whether this is a BOINC, Milkyway@Home or TThrottle issue.

Lastly, what do you mean by "Plan Class an Use"?

Restarting TThrottle does drop the temperature down to the limit I've set with gpu utilization at about 55% or so for each Milkyway@Home gpu task.

I joined the Milkyway@Home project today it queued about 10 gpu tasks for my Nvidia 260GTX, driver 270.61 on Win7 64.
After the first task finished and second task started I noticed that the temp of my gpu was increasing way over the limit that I had set on TThrottle.
TThrottle was stating that it was throttling the gpu at 2%
The only solution I could find was to restart TThrottle. Even the general throttling in the rules tab had no effect.
After this second task finished, the same thing happened with the third task and so on. Since the tasks last just over 25mins, it would be a pain to manually restart TThrottle each time a task finishes.

At first I assumed that TThrottle wasn't aware of the first task finishing and the next starting, but the PID in TThrottle was the same as the PID in task manager and the task name was the same as BOINC's.
TThrottle works fine with GPUgrid on this PC