Maptitude's routing algorithm is relatively slow. Although an individual route calculation typically takes a second or so to compute, a table with thousands of routes can quickly add up to hours of computation. Unfortunately there is little that MileCharter can do to improve the raw processing speed, but this page describes a number of possible approaches.
If you have selected Microsoft Excel for output, setting the Hide Excel during processing can also result in a small increase in speed if you are running on a single-core computer or a computer constrained by cpu usage.
Only Report the Closest Locations
Do you only need the shortest routes, or only those within a certain distance or travel time? If so, use the Only report shortest/quickest routes option. This option only calculates the routes that have a chance of meeting the specified criteria. Exact speed-ups vary and depend on a number of different factors, however, reducing the number of required locations will typically result in significant speed increases. Applying and reducing the distance and/or time restrictions will also result in faster processing.