Yes, HF or other similar notchers (even the more expensive ones) often need a bit of shimming to make them work right. Problem is, any little bit off, even due to "stack" tolerances that are individually within spec, multiplied over the length of the bar, can get it off by 1/8" or more easily. Mine is pretty close but not perfect.
Here is another bit of advice. Cut it first. Figure out where the base of the fish-mouth will be, and add about 1/3 the width of the tube you will be joining. This way the saw only makes half the cut, and you don't wind up with razor edge ears that have to be ground down anyway. Saves the saw which lasts twice as long, and even if it's off a little bit, it doesn't really matter.