I've noticed the behavior as well, it will happen every time the following steps occur, but I've always assumed it was in the Linden code. I never run the stock viewer, but will be glad to if you'd like me to check for the bug there.
Steps to reproduce:
1. Begin an IM session with another avatar. It can be started by either avatar.
2. Make the window as short as possible (showing only four lines of text).
3. Receive a group IM or a conference IM. (The window expands as soon as the message is received, there is no need to switch to the new tab.)
I have attached screenshots following step 2 (IM_Window_Pre_IM.png) and step 3 (IM_Window_Post_IM.png).
(NB: I added some text after step 1 to clear out old private messages so they would remain private.)
My current system, running Debian testing:
(It happened on my older computer as well--Linux 64/core duo/nVidia 8800).
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Cool VL Viewer 1.23.5 (22) Jul 14 2010 16:04:59 (Cool VL Viewer)
RestrainedLove viewer v1.23b (Cool VL Viewer v1.23.5)
Release Notes
Built with GCC version 40102
You are at 147514.7, 279848.6, 1500.3 in Connemara located at sim3805.agni.lindenlab.com (216.82.14.6:13002)
Second Life Server 1.42.0.208314
Release Notes
CPU: Intel(R) Core(TM) i7 CPU 930 @ 2.80GHz
Memory: 12038 MB
OS Version: Linux 2.6.32-3-amd64 #1 SMP Wed Feb 24 18:07:42 UTC 2010 x86_64
Graphics Card Vendor: NVIDIA Corporation
Graphics Card: GeForce GTX 470/PCI/SSE2
OpenGL Version: 3.2.0 NVIDIA 195.36.24
libcurl Version: libcurl/7.16.4 OpenSSL/0.9.7c zlib/1.2.3.4 c-ares/1.4.0
J2C Decoder Version: KDU
Audio Driver Version: FMOD version 3.750000
LLMozLib Version: [LLMediaImplLLMozLib] - 2.01.35017 (Mozilla GRE version 1.8.1.18_0000000000)
Packets Lost: 111/35718 (0.3%)
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Edited to add images that are small enough to upload.