It may take a bit of experimenting but eventually if you screw around with the Cadence options you will arrive at optimum settings for your MIDI rig.
If anything really screws up with Linux sound the best thing to do is remove the offending audio drivers and reinstall them. That will usually reconfigure everything properly on the reinstall.
Sometimes in order to get pulseaudio to recognize a device you have to run alsamixer in a terminal window from the command line to enable a capture. Don't ask me why. It just works that way. That's the problem with one OS and 3 or 4 audio layers.
Same thing with WINE. There are a couple of versions out there and it may help to install the KXstudio version of the program over the default ubuntu one.
Either way you can switch back and forth between versions until you find the one that works best for you.
Synaptic makes all of these switcheroos easy as pie. Just be careful if you start using complete removals. Abort if you see a complete removal involves trashing like 200 dependencies.
There's actually like 4 different layers to Linux Audio these days on Debian based systems.
You've got Alsa, Pulseaudio, Jack, and currently they're running something called Phonon.
They're all quite hackable and can be beaten into shape with sufficient googling and command line editing, but they can be stubborn at times, requiring multiple reboots to get the changes to stick sometimes.
Congratulations young man. You're learning the joys of Linux Administration on the job
Like I said, installing all the KXstudio packages with a meta install and then running KXStudio Welcome from the System Menu will take care of most of the configuration for you.
After that you can tweak as you like.
One of my favorite things about Linux is that no matter how much you abuse it you can pretty much always recover the system even when you f*** things up real bad
I've been running Linux only systems since 1998 so I've learned a trick or two