My N900 also does the same thing:
Occasionally, even though I have the "keep display lit while charging" checkbox, the screen will shut off according to the 1-minute timeout I have set--even while the battery is still charging.

Of course, this issue doesn't come without it's share of other bugs that manifest themselves at the same time as this issue, such as my virtual keyboard missing highlights on pressed buttons, general device slowness, and sound stuttering issues.

Rebooting a few times solves it for me, but every once in a while a reboot would cause my reported battery level to go down to an unacceptable level (around 15%, warning beeps and all...), so I'll use one of the cleanup scripts around here to restart hildon-* and a restart of bme usually fixes all my issues without changing my battery level.

These issues usually only show up after a few weeks of uptime, however, so it's not too big of an issue for me.