I figured out how to work it last time, but a lot of people didn't. I'm sure they would have, its not like its hard, just confusing when things are suddenly and unexpectedly different.
How about an announcement with a short primer.
When someone logs on after not visiting in a while, clicks the new posts button and has 40 pages of a 1000 unread threads, they might get confused, irritated, etc, start complaining and PMing mods. If instead they knew right away, that you can mark all forums read and then click new posts button and have a manageable amount of recent activity, it might make the transition much easier.
"No free man shall ever be debarred the use of arms."- Thomas Jefferson