Software

As far as we know there are 2 main pieces of software that were used by Panchiko in the early days, exclusively for sequencing the instruments and VS-840 via midi

Andy has said that they're not sure exactly which pieces of software were used out of the 2.

Emagic Logic 4
it's fairly safe to assume they were using Logic at the time rather than cubase as Andy gave a particular version (that release in 1999) when asked about what they were using at the time.

(Mac version, Andy most likely used the Windows 98/2000 version)

Old Cubase (version wasn't stated)
The version of Cubase that was out around the time Panchiko were starting to sequence their music was Cubase VST 3.7, and cost a hell of a lot more than Logic (Cubase was over £300), with this in mind i'd assume they probably used Logic