After returning to Megaton through the Super Duper Mart way I encountered an Enclave Solider who blew my head off. I also had a similar experience in the DC ruins however Dogmeat saved the day. Has anyone else had an experience like this? I presume that they are random encounters.

@Wanderer - I noticed this after Broken Steel. I see them occasionally trying to attack Project Purity, and I'll occasionally catch them outside of the Citadel. Fortunately, I have some bad-butt stuff on my main profile including a Gatling laser and the Winterised Power Armour from Operation Anchorage, and I often destroy them.

I had around 11 rounds left so I had to take the solider on with a baseball bat, didn't end well! I never noticed this happening with the original Fallout 3 version however I am now playing the GOTY so it must be because of Broken Steel.

Haha, yeah - if you're going to melee someone in power armour, best to do it with an Auto-Axe or something similar.

Yep. You'll also notice the forcefield is in place around project purity at the start of the game (Though hopefully not switched on).