Hello,
To my recollection, there have been only two threads about this since the game's release, neither of which had any solutions to them. (Actually, most of the replies were of people confused as to what was actually being described, though if I remember one person posted an animated GIF showing what was going on.) In a nutshell, the interior lights (the caged lights on the ceiling and on the walls in the sonar room) would blink on and off in the Type 9 submarines at regular intervals, around once every three seconds.
For a while, I had this problem, then it disappeared until last week. After believing it to be a mod, I reinstalled SH3 with just the 1.4b patch, and it still happened. It occurred to me that I hadn't deleted the SH3 directory where the save games and preferences are.
After lots of trial and error, I finally found out that, strangely enough, it was the 'particle density' setting in the video settings which was causing it. I had set it to 85 a few weeks ago and had continued another career in other sub types. Only this week did I realize the odd behavior was back.
Interestingly enough, if I set the slider to 0 (and restarting the game), the lights in the control room don't come on at all, and the lights elsewhere stay on. The ambient light remains.
Anyhow, I'm hoping to get a few screenshots and perhaps a Fraps movie that better explains what's visually going on. It is likely a rare problem (given only two people in my memory has posted about it, not to mention it only happens in one submarine type) and I can't remember the key search phrase as to make it easily findable on the website.
So, I guess it's a bug that can be replicated, but also can be solved by leaving the particle slider bar at 100. I have an ATI Radeon 9800 and am running windows XP on an Athlon XP 2200. My Catalyst version is 5.6, but this problem has happened back using 1.2, using the Catalyst 5.3 drivers in early April, I'd assume. I've also tested it on an Athlon XP 3400 with a Radeon 9600XT with the same results, using Catalyst 5.4.
Even though the bug (or rather, odd graphical glitch) can be avoided, this is an answer to the two other people who ran into it months ago, assuming they're still around and/or experiencing it.
I suppose it's not that annoying, though at night it's like the boat is on 'red alert' with the blinking.