Why the difference?

I've seen considerably more than two lengths. If you look at Stderr output listing on the task page after an FGRP4 job is finished, you can see two things which so far agree with each other and which come pretty close to classifying the relative execution time needed:

One is stated as showing how many skypoints there will be, in a line like this which can be found a dozen or so lines past the very beginning shortly before the big gaps start:
% Sky point 1/3

The other is near the very end, and is the last of a sequential set indicating checkpoints, with the last one looking like this:

% checkpoint 3
% Time spent on semicoherent stage: 4148.8073s
% Writing semicoherent output file.

% Following up candidate number: 1

and so on for five candidates...

Once I noticed the skypoints number, which is recently, it so far has matched the maximum checkpoint number, or been one more.

On the "production" FGRP4 work, I have seen work units with at least the following number of skypoints.:

3
5
7
12
13
16
19
20
21
23
30

Of these, the 30 checkpoint/30 skypoint type is by far the most common, so far.

Gary Roberts or another guru has indicated that these smaller jobs are termed "short ends" and perhaps a search on that term might give some insight into why these exist. I confess I don't know.