This is quite odd. What are your gutters made of?
Mine are all aluminum, with crimped elbows. They don't leak. I don't understand how/why you would have pin-holes in new flex-elbows?
As for a sealant, I'd recommend Sonneborn NP-1. I doubt the box stores carry it, but check. It's not silicone, but urethane. Bonds tenaciously (sp?) to metal, wood, glass, shingles, concrete, brick, etc.
I used this when I re-roofed my house last Summer.