I don't believe this is an issue with the plugin itself. I've tested both of these things successfully on two separate forums. All I can think of is that other settings/plugins are conflicting with it. I also use is on my own site, on which the users aren't reporting any problems (at least after I introduced the "clear notifications" feature

)
To debug bug #2, go into the threadread table and see if all records for your username have the same timestamp. If not, then the discrepancy is what the system is picking up as a new thread.
Try the memcached version- it's a lot better!