The original remote sends the same sequence over and over as long as you hold it pressed. This particular remote sends an unusually long sequence, so that a short press is few copies of the sequence.

The Pronto tries to detect the repeat pattern, but it might fail for various reasons, including seeing too few copies.

In your first sample above, there are exactly two copies and the Pronto didn't see the pattern, so it recorded exactly what it saw in will play back exactly two copies every time the signal is used.

In your second sample above, the Pronto saw multiple copies and detected the pattern, so it stored only one copy but with an inication that it is one copy of a repeating pattern, so that the number of copies sent when you use that signal will vary depending on how you use it.