Despite what I've seen on some authoritative sites on the effects of Hydrogen Cyanide (some say it's less acidic than even fruit juices), I prefer to rely on what OSHA has to say:
Synonyms: Hydrocyanic acid; Prussic acid; Formonitrile; HCN
Potential Symptoms: Asphyxia and death at high levels, preceded by seizures, coma with abolished deep reflexes and dilated pupils, paralysis; weakness; dizziness; numbness; tremor; loss of visual acuity; headaches; nausea, vomiting; loss of appetite, weight loss; increased rate and depth of respiration, or slow and gasping respiration; eye irritation; rash, chemical burns on skin; enlargement of thyroid gland
Health Effects: Acute Systemic Toxicity (HE4); Cumulative systemic toxicity---weight loss (HE3); Irritation-Eyes, Skin---skin
Affected Organs: CNS, cardiovascular system, thyroid, eyes, skin.
I also assumed that the pill didn't kill him because it had been defective in some way. Though he said it burned his insides, and OSHA states it can cause burns in a high dose, he may have just said this to over dramatize what it did (Silva was certainly big on over dramatizing). It's also possible that even if the cyanide did only minor tissue damage in his mouth, his captors may have tortured him further by not medically treating him which could have resulted in causing pervasive dental disease and bone tissue rotting. Also, people who have survived cyanide poisoning can have brain damage, which would explain some of Silva's extreme behavior.