Need Help Identifying Characteristics of Vinegar in a Carolina BBQ Sauce
The way that brands of the same kind of vinegar can vary is often water content, i.e. the concentration of acid in the vinegar. Some will be more concentrated and therefore more acidic than others, when you switch to a vinegar that is more concentrated than another your result is more acidic and therefore harsh. There's no real standard or rule that I know of when it comes to vinegar strength, and it's not on the labelling, so it's hard to know what you're getting. In general I've found store brands to be weaker than more expensive brands, so I think you're getting inconsistent results because of inconsistent acidity in the vinegars you buy. 

If you are going to get a consistent result you need to develop a method which will compensate for the inconsistency, there's more than one possibility that comes to mind:


Be scientific and use PH strips to measure the acid content of the vinegar you are using. Measure the acidity of the vinegar you've had the best success with and then add water to a stronger vinegar in order to make the PH match. You could also get an expensive electric tester for this but PH strips are cheap (a hundred for less than $10), reliable and accurate
Use your sense of taste. If you are using a stronger vinegar you'll need less of it, so start with a lower amount, say half, then add small amounts until it has the flavor you want. The consideration with this method is that adding less vinegar means less liquid overall, giving you a thicker sauce. You'll probably want to add a bit of water to compensate for that, but when you do it will dilute the flavors, including the acidity


The scientific method's main benefit is that it gives you the most consistency, you'll get the right acid balance every time without guesswork. One's sense of taste can change significantly depending on many factors, for instance if you have a cold, what you've eaten recently, even mood, so if absolute consistency is what you want then a bit of chemistry is the way to go.