Audacity 1.3.12 and Audacity 1.3.13 svn
Linux (Ubuntu 9.04)

Easiest way to reproduce this problem is with a "naughty" Nyquist function:

1) Open Audacity
2) Import or generate some audio
3) From the Nyquist prompt run (lowpass8 s <frequency>) where <frequency> is greater than half the sample rate.
Not surprisingly this produces rubbish (all sample values set to -1.0)

4) Undo everything (or "File menu > New", or delete the track)
5) "Generate menu > tone" does not work.
(all sample values set to -1.0)

This problem persists until Audacity is restarted.
This does not occur with Audacity 1.3.11