Recent call/event notices won't go away

Question

I've got a weird problem with Skype 4.2.0.11 (and previous versions). When I sign in, notifications of recent calls appear like so:
 (contact list)
 (tray icon)
When I click "Mark All Viewed" or the 'X' next to each notification, the notification clears as it should. But when I sign out and sign in again after clearing them, the notifications reappear just as if I hadn't cleared them. 
Any idea what's causing this or how to fix it?
I'm running Linux Mint 14, but have seen the same behavior in Ubuntu 12.10.

Answer 1

The script below will erase all history. Use it when not logged into Skype and do adjust the PROGDIR1 and WORKDIR variables.
PROGDIR1=/home/Skype/SkypeClear
WORKDIR=/home/Ben9999/.Skype
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/bistats.db "delete from Reports;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/bistats.db "delete from Events;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/bistats.db "delete from Sqlite_Sequence;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/bistats.db "insert into "Sqlite_Sequence" values('events',1);"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/bistats.db "insert into "Sqlite_Sequence" values('reports',1);"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/bistats.db "vacuum;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from CallMembers;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from Calls;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from ChatMembers;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from Chats;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "update Contacts set Avatar_Image = NULL;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "update Contacts set Saved_Directory_Blob = NULL;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from ContactGroups;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from Conversations;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from Messages;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from Participants;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from Videos;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "delete from VoiceMails;"
$PROGDIR1/sqlite3 $WORKDIR/Ben9999/main.db "vacuum;"
find $WORKDIR \( -iname chatsync -o -iname "*journal" -o -iname "*.lck" \) -exec rm -fr {} \;
find $WORKDIR -exec touch {} \;