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You are putting a several hundred amp load on the charging system which it was never designed to handle, that is the host car. If polarity is reversed then you are feeding that amperage BACKWARDS through the car being jumped. That can short out the injectors and fry the computer as well as other things.
Do you see burn marks or craters on the battery terminals from the jump start. This would indicate polarity reversal. I don't want to predict what could happen, my knowledge is 2 decades old. The car was a 280ZX and it was jump started backwards, the injectors flooded the cylinders with liquid fuel, so they pushed it to 30 mph and dropped the clutch which bent three connecting rods, leaving 60 psi compression on 3 cylinders with practically no leakdown.
Now we have an engine to disassemble, a fuel injection system that has a lot of melted stuff including the CPU. This was the Colonels sons and his father told me I was a lying SOB when he got the estimate for $5k with out a firm bottom line, since you have to bring systems on line to see what else is messed up. He came and got his car, I called a cop to make sure I didn't kill his stupid ass and the son called me the next day to admit everything I had said was true, even though he watched the whole confrontation and his chickenshit father didn't have the balls to apologise.. An incident I'll never forget and one that convinced me to find another way to make money after 32 years. I started building houses and never looked back.
I'm glad the cop was there and glad I never fixed his car.
Basically you have to crawl through the malfunctioning systems, bringing them on line then continuing until everything works. This assumes the worst case scenario. I hope that is not your situation, but the crazy symptoms are a good indication.