Wondering if anyone else experiences this 'flip'
 

I don't always see this happen, but when it does it is usually after running SH4 for several hours.

In this particular case I inserted a spy in Japan. That mission ran for days and the insertion required waiting to do it in the stealth of darkness.

The insertion was near the bay that Tokyo is in so I backed out of there, went past the small islands across from my bay, and went into the next bay to draw attention away from my drop.

I took on a juicy merchant, nailed it with a torpedo, and finished it with my guns. While we pursued him we got a hit of a second merchant, this is definitely happy days. After dropping the merchant I went in pursuit of the second target with what looked like a convoy getting added to my collection of targets coming in the bay. I followed my merchant and got the sub in position. We had to sit in position much for several hours.

Now comes the flip. I put my scope on the target and went through the process of setting up my torpedoes. My lock indicator was red at the time however it was a steep angle to the west so I wasn't concerned. However at the proper angle it still read red and if I switched to aft torpedoes it was yellow. This is in spite of the fact that the target was in front of me not behind me!!! In a test I found that if I save my game while the ship is still in sight, exit to Windows, then restart the game my torpedoes operate correctly.

That has never happened to me but I usually take a much narrower angle. Did you look at the attack map and see if the track looked messed up?

I still use auto targeting after all these years. I don't remember that happening to me. What version of game are you running, and are you running any mods?

Well I think after so many years the 'version' of SH4 is only 1.5. Though this is the Gold version which adds more models but does not change the base executable. (or should not)

I have the "beginners" list of mods installed.
Webster's GFO Mod v1.1
1.5_OTC for 16 to 9 Aspect Ration_TMO
Webster's New Orders Bar Menu for v1.5
Magnified Hud Dials for v1.5_Large
Webster's Improved US Torpedo for v1.4 and v1.5
SCAF for SH 1.5
Metric Nomographs
MaxOptics3 for SCAF 1.5
Webster's New sonar view for v1.4&v1.5
Data
Webster's Eliminate Floating Plankton for v1.4 and v1.5
SH5 water for SH4
Webster's Upgraded Deck Gun for v1.5
Remove grain effect
FalloftherisingSun_V1.2_SH4V1.5

There may be a conflict with your mods or a corrupt mod file. I did see in the list one that just says "Data." That doesn't seem right. Try re-installing them one at a time until you repeat the problem. A little warning, expect it to take a long time. Good luck.