Why does my Velveeta queso dip get clumpier the longer it stays in the microwave?
From what you're describing, I think the cheese (or cheese-like substance, in this case) 'broke' ... that is, the oil separated out of it.

I'd recommend:


Don't melt it at full power
Stir it multiple times during melting
Melt the cheese (or "cheese-food") seperately, then add the tomatoes, so the tomatoes don't get hot, causing uneven heating.


I'm not sure if there's a good way to recover cheese once it's broken.  Some starch will help keep dairy from breaking in the first place, but I don't think it'd help you in this  particular case.