I'm wondering if anyone else has ran into this issue?

Transcripts are logged fine back to a certain date, and then there simply isn't anything beyond that point. In this case, all the transcripts between the end of February and June are logged, only a handful of the actual transcripts are logged in from December to February, and nothing is logged at all before December.

EDIT: Sorry forgot to mention, this was the upgrade path:

3.4.1 11/12/07

3.4.2 12/13/07

3.4.3 1/3/08

3.4.4 1/21/08

3.4.5 2/19/08

3.5.1 - precise upgrade date is not known, unfortunately.