It's so weird to report Amarok issues, but the 2.9.0 release early this year was a beautiful and hopeful surprise. There is no replacement for Amarok.

I just noticed the same behavior, the STATISTICS table of the MySQL database isn't updated for every track played (accessdate, score, rating, playcount). Applying "MP3 Diags" over some of those track files is enough to make Amarok behave as expected but for some tracks this doesn't make the trick. For those "pesky" songs I've noticed; the reproduction progress bar stops counting at about -0:05 before changing to the next track on the Playlist no matter how the Track Progression was set.

I've been using the same Amarok generated MySQL database since 2013 (Lost the previous one on a failed migration ). Just in case is relevant, the table ADMIN has the following content:

component --> version
AMAROK_TRACK --> 13
DB_VERSION --> 15
AMAROK_PODCAST --> 6
AMAROK_USERPLAYLIST --> 3
AMAROK_BOOKMARKS --> 4

My system:

Amarok 2.9.0
Operating System: KDE neon 5.14
KDE Plasma Version: 5.14.4
Qt Version: 5.11.2
KDE Frameworks Version: 5.53.0
Kernel Version: 4.15.0-43-generic