There is a point when melting chocolate in the microwave or any other way that you can actuall overcook or scorch the chocolate. That's what it sounds like to me when you said it gets thicker.
Just to be safe, mix every 30 seconds in the micro. Even if it looks like it's not melted at all, give it a mix. Mix for a couple seconds before putting it back in though because the chocolate will continue to melt. When there are just a few lumps don't put it back in until you've stirred thoroughly. It may be properly melted, if not then pop it in a few seconds longer but not the entire 30 sec.
Almond bark will not be runny, it's a fairly thick liquid. You really don't want it to be too thin when dipping pretzels or anything else. You need some sort of thickness to get it to stay on what you're dipping.
Michelle