There's any clue on why Battle Programmer Shirase ended so abruptly? I couldn't find any interview or related material about it, even in Japanese. It's sad that is, 14 years already? Without end or an explanation.
If you look at the archived episode guide link for the series, you'll notice that it mentions "part one", implying the series was originally planned for at least another part.
No specific reasons were publically give for the cancellation. Internet rumors speculated that either something happened in production, where someone upset the wrong person high up, or something like that. An alternate theory suggests it might be due to the content, particularly with matters involving Misao's age and the recurring lewd hijinks surrounding the main character (who is about 28)and here. None of these rumors have been substantiated in any way.
It's important to note that the series aired late at night so it's not something an younger audience might accidentally catch by chance. The multiple segmented short anime broadcast format was experimental at the time and did not do so well and has since been discontinued.
It's important to note that the director's message thanking viewers and mentioning the fansub community were removed from the end of the final compiled episode, which fueled speculation of possible personal disagreement within the production committee.
While there are no longer any archived detail some netizens in Japan, mentioned that the second part was supposed to switch to a regular full episode format like in an OVA format. But none of that materialized. What happened will have to remain unknown.
Interesting but not completely related tid bit. The screenplay and character design for the series shares similarities with a incomplete (R18?) doujin game, Tomurai.
You'll see in the TV series credits the variation of the name I assume to be "JR Sakurajima".
It seems it was reworked to fit the anime.
You can still find bits and pieces here and there thru the archives. It give some slight background not covered on the series itself, like Kei Shirase's blog and America King's website. They are just fun Easter eggs.