Sorry for responding late. In case it matters, the IOIO is potentially capable of up to 9 single-precision PulseInput, where every pair of single precision can form a double precision.
For simplicity, I chose to expose this as 3 single + 3 double, but that's strictly an arbitrary software decision.
The code that does that is here:
The part that says new int[] {0, 2, 4}, new int[] { 6, 7, 8 },
Says "use modules 0+1, 2+3, 4+5 as double precision and 6, 7, 8 as single precision. You can change this to whatever other combination you want (remember that double precision always need to use an even index and would use up the next index too, and that in total you have 0 through 8).
There's currently no API to make that change, you're need to modify IOIOLibCore as explained.