In SH3 Commander's Gameplay Settings>Model Effects I have checked the box for Malfunctions. Each time SH3Commander is used to launch SH3, malfunctions (if any) are randomly generated.
I've encountered a few malfunctions. Some are annoying (e.g., a blurry attack persicope, diesel engines that shut down if Ahead Flank is ordered, setting speed at 2 knots while submerged results in speed rising to 5 knots). Others are potentially deadly (e.g. at the start of one mission, maximum speed under diesel power was just 9 knots

).
I cope with the annoying malfunctions as best I can, but when a serious malfunction occurs (like the inability to exceed 9 knots on the surface), here's what I do. Since I've never had the same malfunction reappear twice in a row, my strategy has been to save and exit, and then to reload the saved game right away. I rationalize this as giving my crew a chance to fix the problem so the mission can continue. [I'm sure the purists would consider this to be a form of cheating.]
I'm curious about how others who use SH3 Commander handle malfunctions. Do you press on regardless, abort the mission and return to base for repairs, save and reload, etc., etc. ?