That is certainly not right... Are you sure you didn't copy the files around or use any photo importer software?
As one would expect, the files are usually recorded serially by number and should be timestamped as such.
Please email us the log files from the affected flights so we can take a look at what is going on here.
In general though, Map Pilot doesn't have any control over what files are named or the numbering of the images since that is all handled within the camera. If we did we would certainly try to do something that made more sense that this!