Yep, it sure is. Different chains need to be treated differently. Some require special pins every time you break them (Dura-Ace), some come with master links that work well, some come with master links that suck...So: It's a good idea to read the instructions that come with the chain.

My experiences:
After 15 years of hard riding and reliable chains I've recently had a rash of broken chains on my mountain bike. Multiple chains, some LX-level Shimano, one a Dura-Ace, and the latest was the high-end SRAM. I use a Park chain tool, and have (until this rash of problems) a flawless chain install record so installation shouldn't be the problem, BUT:

I finally figured out the common problem: mushroomed chain breaker pin. When I would retract the chain breaker the pin would catch on the outer plate, pulling it out a bit and probably deforming the hole. After the chain was re-joined, the rivet wouldn't press-fit into the outer plate securely, and after a bit of use the chain would break at that spot. The last time this happened I used the chain tool on my Crank Brothers multi-tool which has a new pin in the chain tool (excellent multi-tool BTW) and haven't had a problem.

Long story short: make sure the pin in your chain tool isn't mushroomed from use. The good news is that they're cheap and easily replaceable. I'm going to buy 3 today.