Yes. You can use QuickTime Text Descriptors to accomplish this. What you need to do is add the following tags immediately after each time code in your transcript, like so:

[00:01:00.00] {scrollIn: on}{continuousScroll: on}
This caption will scroll.
[00:02:00.00] {scrollIn: on}{continuousScroll: on}
This caption will scroll as well.

Note that the “{scrollIn}” and “{continuousScroll}” commands need to appear on every caption. This is simply the way that QuickTime works. You can easily do a Find and Replace to insert them after each time code (e.g. if you’re careful about only using “]” for time codes, just search for “]” and replace it with “] {scrollIn: on}{continuousScroll: on}”.

You may need to play with the timing a bit to get the right effect. Note that scrolling subtitles work well if you place them beside the video: use the custom position setting in the Export Subtitles dialog to place them properly.

You can also do horizontal scrolling like so:

[00:00:00]{scrollIn: on}{continuousScroll: on}{horizontalScroll:on}
This caption will scroll.
[00:00:05]{scrollIn: on}{continuousScroll: on}{horizontalScroll:on}
This caption will scroll as well.
[00:00:10]

Though again, you’ll want to play with the timing and commands to make sure the scrolling works as you want.

For a full list of text descriptors you can use, see http://www.apple.com/quicktime/tutorials/textdescriptors.html.