Don't feel bad about it, even water 'experts' such as A.J. DeLange and Martin Brungard get into disagreements on water chemistry.
First, you are saying that the pH reading on your water report is different from the last report? OK, don't sweat it. The pH of your base water only has a minor impact on the buffering capacity of the ions in the water by determining the form the carbonate ions are present in.
Second, the comment about the mash water acid appears in every brew sheet printed. It is in the base HTML in which the report is written.
Next, your water profile only impacts the prediction of mash pH in BeerSmith IF you have entered your water report as a profile in the water ingredients and IF you have added that water profile to the recipe as one of the ingredients.
Now, if you are doing all-grain brewing and want to endure better efficiency from your grains, you would be on the right track to get a pH meter and measure the pH of the mash. The (arguably) best place and time to measure the pH is about 15 minutes into the mashing, at the draining of the first runnings and at the end of draining the sparge water. An alternative to the pH meter would be pH test strips. They work OK do not have the precision of a meter in most cases.
The reading at 15 minutes into the mash it to make sure you are within the desired range for best conversion [5.2 to 5.6]. At the end of the mash, the reading is to ensure you are still within that range, as the pH will change based upon the minerals in the malts and the types of malts in your grain bill. If you are doing a fly sparge, many brewers will check the pH of the run off to ensure it does not go above a pH of 6.0 as the combination of high temperatures (above 170?F+) and high pH will help in the release of tannins from the malt husks.
While there is some confusion about the actual measurement temperature, the correct method is to take a sample and chill it down to room temperature and then take the pH reading. While pH meters will come with ATC or 'automatic temperature correction,' this is often mistaken for correcting the pH to room temperature. The correction is actually a correction on the electronics inside the pH meter to the calibration curve of the probe to negate the effect of high (or low) temperatures on the slope of the calibration curve.
You don't necessarily need to invest in a high priced pH meter, though those are much more reliable. I would recommend getting a model with automatic calibration, though. Models where you need to calibrate the meter manually using a screw are often difficult for those who don't know how to make the adjustments and unreliable in holding that calibration. Even then, I would look at a pH meter which costs less than $40 or so as a disposable piece of equipment, needing to be replaced every year or so when it becomes difficult to calibrate. Even with expensive pH meters you will need to replace the probe on a similar basis. I've been using the same $20 model for about a year now and it is working fine. I do need to calibrate it every time I use it though as it does drift quite a bit.
Once you have a handle on what your mash pH is in some cases, then you have a chance to learn how to modify it to change the pH of the mash and accentuate flavors in your recipes. I highly recommend looking at some of Brad's blogs and interviews on water chemistry and reading Martin Brungard's primer on 'water knowledge' which can be found on his web site at https://sites.google.com/site/brunwater/.