I have this problem too.  It did not occur until I upgraded to Hardy.
With a feed selected, I hit ctrl-R to mark all as read and this is marks
all messages as read in the list of feeds to the left.  However, some
items in the list of stories in the feed I'm reading (right panel)
remain bold until I switch to another feed and then switch back.  I
don't see any pattern as to which stories stay bold, though this
behavior only seems to happen when I mark all as read in a feed with 30+
new items.

I'm also using a copy of my config file from Gutsy and running the
PowerPC version.

-- 
liferea mark as read, does not always mark all as read
https://bugs.launchpad.net/bugs/216720
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