If we had any doubt on this Shabbos we immediately start the medicine since he is now a Choleh. Thus if it is a short course we can start immediately since he is now in danger. The Gemara is discussing where now there is no immediate danger but there could be danger the next Shabbos if we delay and therefore we have the Safek of whether to wait in order not to be mechalel two shabboses. (Meiri, Ran Shabbos 40a)

The son of the Maharal raised this question (Shabbos 40a) as well in his chiddushim on the Rif and he answers in his father's name that if it is one Shabbos then for a Safeik we would be machelel Shabbos but for the safeik that on a second Shabbos he might be in danger we don't do chilul Shabbos. The son then asked his father what is the difference between one Shabbos and two shabboses and did not get a clear answer, but it appears that the Maharal also understood that the Safeik for two or three days is an imminent Safeik and therefore it is clear we can be mechalel Shabbos but for a safeik as far as the next Shabbos we would possibly not be machelel this Shabbos.

Yoel Domb