This is exactly what I suspected at the first.
Checked database, all logs on my box, even tables structure (maybe they are corrupted or something). But not... All was pretty much normal.
Today I made simple shutdown with 120 sec. All went fine. Server got closed etc. No errors whatsoever.
After the start it appeared that some dropped items in line 15..20 min before, was not inserted in items table. It looks like it was just in memory/some java threads and simply just not inserted when it suppose to be.
Maybe there is something there? Like items are stored in db to rarely? (Dunno, just made up shot in a dark).