I guess this is the same, or at least related to
Truncate silence does weird things when used on multiple clips in the
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
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.
After selecting the track and before applying Truncate Silence, press
Ctrl+J to join the clips together.