Describing a still working self developed software system in a research paper. Which tense to use?
Question: should I use anything other than the present indicative active tense to describe a system's behaviour. 

Question: is there any reason to write in another tense? Will it help a reader to understand the system better if they think of it as functioning at some time in the past? 

Answers: if you are describing a mis-behaving or erroneous system ("when I pressed button 'B' the system gave off a cloud of smoke") then it would be useful in that it would distinguish the mal-functioning instance. But you are trying to describe a properly-functioning system and so the present indicative active tense is preferable: "Press button B, The green light illuminates ...". It reads like a manual and so your write-up will be useful.