Well turn off the speaker in Skype, you cannot use both at once through
one set of speaker, microphone.

Skype is proprietary software, so it can't be patched by open source
developers. There is not much interest in the open source community in Skype
because it is proprietary and there are several good open source
alternatives, so fixes are not going to happen. An explanation of the
problem is that Skype uses its own drivers and protocols and they are
incompatible with Ubuntu's. Sometimes the transition between the two is not
smooth.

Here is a page describing variouis Skype problems and fixes for Ubuntu:
https://help.ubuntu.com/community/Skype

I've looked at Ekiga and it doesn't talk
to Skype so I wouldn't be able to talk to friends who I haven't been
able to convince to switch to Linux, :-) Also, Skype allows free phone
calls to 800 numbers which allows me to use my computer as a speaker
phone for conference calls with great audio. I just have to put up with
the ribbing I get when someone who I am talking to on Skype sends me a
web page link and doesn't understand why I can't hear the audio that's
playing, but I'll survive.

You are not limited to Ekiga. There is Wengophone or openWengo, SipPhone and
Gizmo5 with OpenSky(pe) which is free and built on open source, but for
profit.

Linux is a whole new world of free (as in freedom) software. Skype is not
part of it. Although it can be made to work, it is still foreign territory.
So you have to decide what you want and what you are willing to put up with
to get it.

This is the whole conundrum that Windows users face when they try Linux. Do
they want proprietary or do they want something that is as good or better,
but is incompatible with what most users are used to? Most Linux users would
not bother with Skype because their friends are either not Windows users and
Linux users don't use Skype or they have found other solutions.

The reason why open source works in your favour and proprietary doesn't is
that open source developers can fix problems if they have access to the
code. In this case they don't.

Convince your friends to go open source and your problem is solved. If I
sound unsympathetic then you can guess that this is probably what most Linux
users feel about proprietary solutions vs. open source.