I guess this is the same, or at least related to http://bugzilla.audacityteam.org/show_bug.cgi?id=116

Truncate silence does weird things when used on multiple clips in the same track.
Using Audacity ® 1.3.12-alpha-Feb 27 2010 on Ubuntu 9.04

Steps to reproduce:
1) Generate a 30 second Chirp with a starting amplitude of 0.8 and an end amplitude of 0.1 (makes it easy to observer the problem)
2) Cut-Delete a number of sections (Alt+Ctrl+K) from the track.
3) Select the entire track and apply Truncate Silence with settings 1,1,4,-40

The result will typically leave a section at the end detached from the rest of the track. The exact results depends on which bits have been cut out, (where the cut boundaries are) but it is always wrong.

Workaround:
After selecting the track and before applying Truncate Silence, press Ctrl+J to join the clips together.

Steve