I've just updated four sites from WordPress 3.0.5 to 3.1 (using SVN), and then updated Nice Search from 0.2 to 0.3 using the WordPress plugin upgrade functionality. I have experienced a similar issue on all of them:
After updating Nice Search, the version stays at 0.2, even though I have just updated, so WordPress says it still needs updating.
So I then update it again, and the version number correctly updates this time, but now the plugin is not activated, even though it was active before update, so I have to manually activate it.
I've not experienced this behaviour with other plugins on the same sites.
It's not a major issue, but thought you may like to know about it.