From aTunes Wiki
Please also see our FAQ
In slider bar, remaining time is wrong with some VBR mp3 files (fixed in aTunes 1.11.1) This is actually a bug in MPlayer. If a VBR mp3 is played back, the total time is computed wrong and thus the remaining time is wrong too. This is a known problem since 2006.
 The value shown in the properties is usually correct as it is determined by the tagging library.
Changing volume while paused will resume track (fixed in aTunes 1.8.3) This is actually a bug in MPlayer. If a track is paused and the volume
command is send to MPlayer the track will start playing. We have a
workaround for this but for a few milliseconds after the volume command was
send the track is playing...
This has been reported as bug 1048 to mplayer team. 
Stopping the song can cause a bad file descriptor error (fixed in aTunes 1.8.3) Only known to happen on some Linux systems. Disable volume fade away to work around this issue (Preferences -> Player tab). The error message seems not to cause further problems. We don't know why this is happening for now.
Characters can appear garbled in tags
Usually occurs in mp3 files, mostly in files with ID3v1 tags. It is caused by various tagging software not complying with ID3 specification and using a wrong charset. Currently no workaround is available.
Not all fields can be written for wma format (fixed in aTunes 1.12.0) This is a limitation of the JAudiotagger library. Only the following fields can be written:
Artist, Album, Track number, Title and Year.
No changes are to be expected soon.
When trying to delete tag fields of multiple files by blanking them, nothing happens (fixed in aTunes 1.11.0) This is a design limitation of aTunes. If we would not do this, fields not edited would be deleted.
No tag is read and volume slider bar does not work for Monkey Audio and Musepack files
This formats are not officially supported. For this to happen, support for those formats must first be included in the JAudiotagger library.
Autofilling an mp3 device throws an "Not enough space on device error" (since aTunes 1.8.3)
The way the remaining memory is calculated is inaccurate and depends on actual files. If you encounter this error either retry or enter an higher value for the memory that should be left free (30MB for example). Reducing this same value increases the likelihood of this error message.
When ripping a CD to Mp4 format using the FAAC encoder, the progress bar is stuck at 0%
This behaviour has been observed on Windows machines and despite long investigation we did not find the reason why this is happening. For this to happen the FAAC encoder must have been installed manually. The same encoder works well under Linux systems. It is advised to use either the Nero AAC encoder or an alternative format like Ogg Vorbis or Mp3 instead.
Autocompletion in the tag editing dialog does impose the case (fixed in aTunes 1.11.0) When changing tag information, autocompletion will not allow to modify the case directly. So one can not change the artist from "ABBA" to "Abba" for example. To work around this, first add any character different than the first at the beginning, save the tag, then make the change you initially wanted:
"ABBA" -> "bABBA" -> "Abba"
After having made a manipulation like editing tags or ripping a CD, songs are missing in the navigator
After ripping a CD or editing tags it can happen that some files do either disappear in the navigator tree or are not added to it. Refreshing the repository should resolve this issue.
Under Windows, changes to the tags are not applied when the song is playing
Currently there is no known solution other than stopping the song. Editing the tag and playing can not be done in the same time.
When starting aTunes under Solaris from the Gnome menu, mplayer can't be found
First of all make sure mplayer is really installed. When starting the aTunes.sh script from the command line, it should work normally. Under Solaris, mplayer might be installed in /opt/csw/bin, if this is the case just create a symlink
ln -s /opt/csw/bin/mplayer /usr/bin/mplayer
Files with .inf ending are created when ripping a CD Cdda2wav which is used for ripping contained a bug which lead it to create such files. Users experiencing this problem should update to cdda2wav version 2.01.01a58 or higher which fixes the problem. The *.inf files can be deleted safely.
CD ripping does not work under Ubuntu when icedax is used
The icedax version which can be obtained through Synaptic is completely broken and does not work properly. Other distributions do not seem affected. Ubuntu users should use cdda2wav instead. Please see Installing dependencies for more details.