[Filthy Slider]

went through every injury of the season in league injury news

checked to make sure that players did not play (as listed in the game-by-game stats section of their individual player page) during the time span of the listed injury...did this only for players hurt on active roster, but did a few random checks on minor league injuries too

only injuries that required time off and day-to-day injuries that should still be effective on June 30 of the season could be checked since players frequently do end up playing during the days in which they are on day-to-day status.

FINDINGS:
2 other injuries that did not 'register'...both were of the day-to-day type and should have been continuing on that status beyond June 30 but were listed in the game as "OK"...both of those injuries occurred on days in which there was a major headline in the news about a major injury which did not take effect in the game.

To be clearer, these were entries in the league injury report:

June 16:
F.Wooten (SL) out 6 weeks [was in the league news and was listed as
"OK" from June 17 on]
J.Franco (BOS) day-to-day with full recovery in 5 weeks
[as of June 30, listed as "OK" status]

June 17:
F.Cabilao (MIN) out 11 weeks [this is the player that hit that HR against
my team that got me to start this thread]
R.Janik (SL) out 7 weeks [has not played since June 17 and as of June 30
is still listed as injured...is on DL as expected]

June 29:
N.Tune (FLA) out 5 weeks [news headline for June 29, as of June 30 listed
as status "OK"]
F.Mariscal (CHI) day-to-day with full recovery in 2 weeks [as of June 30
listed as status "OK"]
M.Ortiz (KC) out 5 weeks [as of June 30 is listed as "out 5 weeks" and is
on DL as expected]

So, it appears that the day-to-day injuries occuring on the day of a newsworthy injury are not being registered while injuries that involve complete time off that happen on the day of a newsworthy injury (except that of the newsmaking injury itself) are being handled properly by the game.

All other injuries that were checked from the legue injury news report were handled properly by the game.

Also, it is of note that there were, in fact, other injuries (all of which were handled properly by the game and did not occur on days of newsmaking injuries) that occurred between the dates of June 17 and June 29.

Well, that's what I've come up with...
For now I just went and used the manager mode editing utility and made all those above players that should have been injured begin 'serving their injury time' starting June 30...and, I will just keep checking the league injury news each day.