Try running the Alpha with Jackd into something like Ardour and see what kind of results that gives you. Ardour is probably overkill for what you are doing but it should at least give you an idea of what is going on. They are in the repositories so just do "sudo apt-get install ardour jackd" and you should be set. You might want to check out
Ubuntu Studio as well. All I did was add the repositories to my installation of Ubuntu and download the low latency kernels and it runs like a dream. Just make sure you do the last step adding the lines to you limits.conf and you'll be rockin'.
http://jackaudio.org/ http://ardour.org http://ubuntustudio.org/