gaim doesn't stop flashing in taskbar.

I noticed this behavior also. Actually, the item in the taskbar stops flashing after text has been typed in the message input field. This is very annoying.

thanks for your bug. What options do you use for the message notification plugin?

Bug report on SourceForge:
http://sourceforge.net/tracker/index.php?func=detail&aid=1544489&group_id=235&atid=100235

I didn't know it was configurable actually...
The option "Remove when conversation window gains focus" was unchecked. I checked it and it worked as expected: it stopped blinking when the window came in focus.

I don't know if it's the same for lexual, but if it is, I would suggest that it be checked by default as it is more natural to me that if the window gets the focus it stops blinking. It is the default behavior of most applications I used in the past, and also if the windows gets focus, most likely you read the message so there no need to keep blinking, right?

See above screenshot.
Note that I haven't changed the default config, and I doubt I would have found it easily without reading Mathieu's above comment.

I would recommend having both click and focus options being enabled.

That's the correct solution for this.
I'm closing this bug as it is a config issue and a duplicate of bug #64518.