The correct decimal separator in srt files is the comma. 00:00:00,000 is the correct time stamp format. VLC Player, among others, requires this. However, some players and editors apparently do not like commas and substitute decimal points, as in 00:00:00.000 and VLC currently will not recognise these.
The "incorrect" 00:00:00.000 Format is still specific enough to cause no problems parsing it.
see viewtopic.php?f=2&t=57989&p=193330#p193324