klinkigt, if it were me with these symptoms, and if I wished to understand better what was happening, what I would try to do is determine what device was using the sound driver during the various instances you describe.
Sometimes, when one has basic sound functioning, but then it appears to stop in the middle of a session (to be restored after a reboot or restored via “rcalsasound restart”) it may be because an application has seized your audio device, and the application is not sharing nor letting go the audio device. To determine what application is using one’s sound device, copy and paste the following into a terminal or a konsole:
lsof /dev/dsp* /dev/audio* /dev/mixer* /dev/snd/*
If one runs the above line at different times, when one’s sound is working and not working, one can learn better as to what the output means, and be better able to " point one’s finger " at the offending application that has seized the audio device.
So I recommend you run that line, and copy and paste and save the output, in each case you described, … ie
when everything works - boot sound, amarok, Skype
when only amarok works
after running “rcalsasound restart”
Then compare the various outputs, to see if you can determine the offending application that may have seized the sound when your Skype struggles. Note I do not use Skype, so I can not offer any support there.
Note that “rcalsasound restart” will typically break the hold of any devices that have inappropriately “seized” the sound device.
Also note that for multiple applications to use the sound device at the same time, typically requires one use the ALSA API, or use Pulse Audio, where unfortunately Pulse Audio is buggy, and its use not very understood by many of us (I include myself in that category).