I am running Windows 10 Home.
I am using Audacity 2.1.2, but I did some processing in 2.1.3 Alpha Jan 7 2017 to use the Speed function. (The Speed function in 2.1.2 rounds the new length so it does not end up being the exact number of samples entered into the dialog box).
I obtained version 2.1.3 alpha from the .zip file. I think that I got 2.1.2 from the .exe installer, as the .zip file is not on my system.
The folder at https://www.dropbox.com/sh/gg2r7hipwfzxfoy/AADUNn6-dRtId-QOLq_zQ0hPa?dl=0 holds examples of the issues I am having and should be publicly available for viewing.
The image glitch-end_of_clip.gif is an example from the end of a 96-minute long file. The source was exported from Pinnacle Studio Ultimate (video app) as a 48K 16-bit .WAV file. The lower stereo track is as exported from Pinnacle and the upper stereo track is after importing the file into Audacity 2.1.3, closing the project and then reopening it. I don’t recall whether I reopened it in 2.1.2 or 2.1.3. There was no length change in this track. Note that the three sections separated by silence are all the same and are the same as the end of the undamaged track. I did not import the track data into Audacity. The total length of each silent segment and the block following it is very nearly 2^10 samples, which may be significant.
The file glitch. WAV is of a short section of misplaced audio at 64 minutes 33 seconds in another 96-minute track. This track was .WAV from a Zoom H4 audio recorder, also 48K, 16 bit. The file glitch.aup and its subfolder are of this glitch. The glitch occurs in Audacity, not in export. This track was the third track and bottom stereo track in a project.
When I split the 96-minute file into two sections, 53 and 43 minutes long in Audacity 2.1.2, the glitch at 64 minute 33 second disappeared but a similar glitch appeared at approximately 20 minutes. I did not import the track data into Audacity.