I vaguely recall a similar issue with an old rev of Audacity, which I think was later fixed. When switching to Spectrogram (Log f) track display mode, if Preferences->Spectrograms->Minimum Frequency (Hz) is set to 0, the values on the frequency axis are initially out of alignment with the display. 60 Hz, for example, might appear at 6 Hz on the frequency axis (this with window size of 2048!). When scrolling horizontally at sufficient rate that the whole display gets refreshed rather than part of it scrolling, the alignment gets fixed. Zooming on the frequency axis also fixes it. Forcing a refresh by going to Preferences->Spectrograms and hitting OK without changing anything puts it back out of alignment. This would be a good way to reproduce the behavior.
I’m running Audacity 2.0.5 Alpha under Vista. Just tried 2.0.4 and it does the same thing. Could be I just noticed this because while testing some developmental revs all my preferences got reset. Normally I don’t have Minimum Frequency set to 0.