@the_safireeye Hi, sorry to hear about your issue.
Please do the following to help us review the problem:
- Download the latest development build that is appropriate for your operating system from the following site
- Create a new file and reimport the sound (it won’t work if you don’t import it again since the sound loading functionality is different in recent versions) If doing that works better let us know.
- Now open your actual animation file, delete the previous sound and reimport the sound again with this new build.
- If the latter works better as well please let us know.
Be aware that for these development builds, you should not scrub over a sound first before trying to troubleshoot if the file is being cutoff incorrectly.
I personally found a bug on the nightly build a few days ago. If you move the timeline cursor partially over a sound and then go back to the start and press the play 
button you will only hear the “rest” of the sound.
On the other hand the sound sync perception is not exactly a bug, but is also not an ideal situation.
For a tutorial on how to import sounds, and do proper lip sync / sound sync with theaudio scrubbing feature please check out this unlisted tutorial I made for another user.
Lip sync explanation up until minute 08:00, the next section is for troubleshooting tips on sound issues related to scrubbing. Hopefully you won’t need those.
Please read the known issues section on this thread for a simple explanation:
For more in-depth explanation please read the reply below:
Regarding audio delay on playback
Playback in Pencil2D works by caching about 1024mb (default) worth of images constructed by the layering of each image track, and then plays it back as smoothly as it cans.
This process however often takes a bit to populate the RAM with the cached images, so you often need to play it 2 or 3 times before it plays smoothly (though I don’t know why it takes a few tries tho )
Pencil2D audio is not currently going to sync during playback regardless of what you do. This happens with every other software as well.
That said other apps work around this by implementing an intermediate “preview” window with pre-rendering techniques that shows a real-time, but low-res version of the animation.
Some apps call this intermediate file or process: playblast, proxy preview or cached pre-render. There are unfortunate yet deep tech reasons for this but it all boils down to:
The more layers and frames you have, the less synced the audio will be. Period.
If you want you hear your synced audio, you currently have to use the audio scrubbing feture (i.e moving the playhead / timeline cursor over the timeline where a sound is laid out) or export a low resolution video from the app for more involved workflows
Note: Pencil2D has a command console access to enable headless rendering. This could be used along scripting features in other apps to automate previews.