Hello cadm8,
Starting from the version 1.3 PhotoScan is utilizing GPU for the image matching process (first phase of the Align Photos operation), so if you have any GPU checked on in the corresponding Preferences tab, then the processing would be faster than using CPU only.
However, in the version 1.3.0, compared to 1.3.1 and 1.3.2 there was the limit to the number of image pairs used for the depth maps filtering. We have removed that limit in the 1.3.1, as in some cases of oblique shooting the noise level was considerable. But that is related to the dense cloud generated, not to the image alignment.
Can you check that you have GPU enabled in the latest version?