"Ar" is used to express temporary physical, emotional or mental states (I suppose to make clear that they're not an intrinsic part of you), so as well as medical ailments, you would also say "mae ofn arna i", "mae hiraeth arna i" ("I'm afraid", "I'm homesick/nostalgic"). However, with the word "tost" you use "gyda" or "gan" (depending on dialect), but the reason for this apparent anomaly is not random: the explanation is that "tost" is an adjective meaning "sore, painful, aching" which is used together with a body part (e.g. "pen tost", "stumog dost" = "a sore head", "a sore stomach"), and since that body part is an intrinsic part of you, it is "with" you rather than "on" you. In other words, when you use "tost", you're not saying, for example, "I have an ailment called headache", but "I have a head and it's sore". This nicely illustrates the difference between Welsh thought and English thought and how important it is to get into the mindset of the language in order to understand its logic.