I don't really understand paint schemes and the like, but I have indeed noticed that on the Q400 the white strobes don't actually flash at night, but are steady. Is this intentional?
The repaint textures don't change anything about the lights (they are controlled through .fx files and the aircraft.cfg), so they are as Majestic released them.
I think a few Majestic customers have reported this behaviour on other forums and I believe it's a bug; http://majesticsoftware.com/forums/discussion/507/white-strobes-stay-steady-on#Item_2
Majestic have informed us that they expect the 1.007 update to be released in about a weeks time, which may resolve your strobe issue. Majestic have yet to provide information regarding what will be addressed in the 1.007 update, other than the "bouncing" problems some users experienced on the ground.
Please remember to back up your settings (the mjc84.ini and also your aircraft.cfg) before installing the update! I'll post a news article when I get confirmation of the update's release.