Increase the analog sample rate of the IOIO?
From Google ioio users group 2011 this extract:

... the line saying

PR3   = 0x07CF;


In the file firmware/app_layer_v1/adc.c should be changed to

PR3 = &lt;whatever sampling period you want&gt;,


where the units are in 0.5 micoseconds.

Another small change you may want to do: the AnalogInutImpl.setValue() method gets called every time a fresh sample arrives from the IOIO. You may want to push them into a queue so that none gets lost instead of just storing the most recent value, as in the current implementation.

appears to be what's wanted.

There is extensive discussion involving this at the above address.

And similar here from August 2012

And probably this too - 2011 again