I've had the same kind of thing, but the betaine-HCL/oxbile combo did such a great job, and since I don't have a gall bladder I really need the stuff.
The trick is that pre-paleo, having taken OTC PPIs, my stomach wasn't producing enough acid, so it didn't use as many minerals. When the betaine-HCL and oxbile was introduced (Now Super Enzymes), it now could, and started to cause problems such as even worse acid reflux (which was temporary), and then intolerance to egg whites, and even twitching.
But in a few weeks, after also supplementing potassium and magnesium, it's as if the whole system adjusted and became a smooth running machine. I also discovered it wasn't just wheat that was causing my reflux, but also cow dairy.
So you might find it takes time to adjust, but when you do, you'll feel much better than you did before.
The twitching is absolutely associated with magnesium, so supplement. I don't bother with potassium anymore since the caps are all limited at 99mg and you get a lot more from food, but modern foods lack magnesium due to poor soil. (I suppose that explains my coffee/100% baking chocolate addiction - these two are high in magnesium, though it's bound by phytates.)
I suspect that betaine HCL and friends kick starts broken stomach acid, which in turn requires more magnesium (and other minerals, hence the side effects) - it's not so much that betaine HCL causes side effects as rather you're depleted, but you don't notice it until you use up more from the increased stomach acid.